From 325b8e5dc5378549c81fb9f41e025ab1611380f2 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 08:52:04 +0200
Subject: [PATCH 01/86] Improving odgi figures
---
config.yaml | 4 ++--
scripts/contig_position.R | 5 ++++-
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/config.yaml b/config.yaml
index f604523..bb630d2 100644
--- a/config.yaml
+++ b/config.yaml
@@ -16,8 +16,8 @@ wfmash.secondary: '-k 19 -H 0.001 -X'
seqwish.params: '-B 10000000 -k 19 -f 0'
# Odgi 1D and path coverage viz parameters
-odgi.1Dviz.params: '-x 2000 -a 25 -b'
-odgi.pcov.params: '-x 2000 -a 25 -O'
+odgi.1Dviz.params: '-x 2000 -a 50 -b -H'
+odgi.pcov.params: '-x 2000 -a 50 -O'
## Optional parts of the workflow
# Running Quast to get statistics on input haplotypes
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 7ccd486..dc3a2ce 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -33,8 +33,11 @@ my.cytobands <- toGRanges(x)
# Creating figure
# Customizing figure parameters : see https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html
pp <- getDefaultPlotParams(plot.type=1)
-pp$ideogramheight <- 200
+pp$ideogramheight <- 50
pp$data1outmargin <- 50
+pp$data2outmargin <- 0
+pp$data1inmargin <- 0
+pp$data2inmargin <- 0
pp$leftmargin <- 0.28
pp$rightmargin <- 0
pp$data1height <- 0
--
GitLab
From 9a10808d2453923cb8962ea8a585f77dd01485cf Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 09:32:35 +0200
Subject: [PATCH 02/86] Continuing to improve figs
---
config.yaml | 4 ++--
scripts/contig_position.R | 6 +++---
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/config.yaml b/config.yaml
index bb630d2..05de181 100644
--- a/config.yaml
+++ b/config.yaml
@@ -16,8 +16,8 @@ wfmash.secondary: '-k 19 -H 0.001 -X'
seqwish.params: '-B 10000000 -k 19 -f 0'
# Odgi 1D and path coverage viz parameters
-odgi.1Dviz.params: '-x 2000 -a 50 -b -H'
-odgi.pcov.params: '-x 2000 -a 50 -O'
+odgi.1Dviz.params: '-x 2000 -a 150 -b -H'
+odgi.pcov.params: '-x 2000 -a 150 -O'
## Optional parts of the workflow
# Running Quast to get statistics on input haplotypes
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index dc3a2ce..9ac8182 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -33,9 +33,9 @@ my.cytobands <- toGRanges(x)
# Creating figure
# Customizing figure parameters : see https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html
pp <- getDefaultPlotParams(plot.type=1)
-pp$ideogramheight <- 50
-pp$data1outmargin <- 50
-pp$data2outmargin <- 0
+pp$ideogramheight <- 100
+pp$data1outmargin <- 25
+pp$data2outmargin <- 25
pp$data1inmargin <- 0
pp$data2inmargin <- 0
pp$leftmargin <- 0.28
--
GitLab
From a29eff609cbf481963b432fdd62f42a957da81c4 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 09:38:28 +0200
Subject: [PATCH 03/86] Update contig_position.R
---
scripts/contig_position.R | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 9ac8182..1d6fed9 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -23,6 +23,7 @@ x = read.table(opt$tsv, sep = "\t", comment.char="^")
colnames(x) = x[1,]
x = x[-1,]
my.genome <- toGRanges(x)
+nChr = ncol(x)
#print("Reading bands file ...")
x = read.table(opt$bands, sep="\t", comment.char="^")
@@ -43,7 +44,7 @@ pp$rightmargin <- 0
pp$data1height <- 0
pp$data2height <- 0
-png(opt$out, width=2780, height=500, pointsize=6, res=300, antialias = "none")
+png(opt$out, width=2780, height=(nChr*150), pointsize=6, res=300, antialias = "none")
kp <- plotKaryotype(genome=my.genome, cytobands=my.cytobands, plot.params=pp, chromosomes="all")
kp <- kpAddBaseNumbers(kp, cex=0.6, tick.dist=5000000)
dev.off()
\ No newline at end of file
--
GitLab
From 47c4dce4ff50a4eeb41de9f3551aaaacc9f387b9 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 09:46:58 +0200
Subject: [PATCH 04/86] Update contig_position.R
---
scripts/contig_position.R | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 1d6fed9..0639c1e 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -23,7 +23,7 @@ x = read.table(opt$tsv, sep = "\t", comment.char="^")
colnames(x) = x[1,]
x = x[-1,]
my.genome <- toGRanges(x)
-nChr = ncol(x)
+nChr = nrow(x)
#print("Reading bands file ...")
x = read.table(opt$bands, sep="\t", comment.char="^")
--
GitLab
From 7fd84f0322c67dfaa1849f2d162f23d90ab90121 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 09:55:18 +0200
Subject: [PATCH 05/86] Update contig_position.R
---
scripts/contig_position.R | 2 ++
1 file changed, 2 insertions(+)
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 0639c1e..d367beb 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -41,6 +41,8 @@ pp$data1inmargin <- 0
pp$data2inmargin <- 0
pp$leftmargin <- 0.28
pp$rightmargin <- 0
+pp$topmargin <- 0
+pp$bottommargin <- 0
pp$data1height <- 0
pp$data2height <- 0
--
GitLab
From 6515a5349ca140ab1156dcd4eabd30098d78f0c1 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 14:49:01 +0200
Subject: [PATCH 06/86] Started creating reports
---
Snakefile | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++++
config.yaml | 4 ++-
2 files changed, 78 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 5c775d6..1a7dae4 100644
--- a/Snakefile
+++ b/Snakefile
@@ -59,6 +59,10 @@ def which_analysis():
analysis_inputs.append(
expand("output/chr.contig/{haplotype}.contig.png", haplotype=CHRLIST)
)
+ if config["create_report"] == "True": # Create report
+ analysis_inputs.append(
+ "output/pan1c."+config['name']+".report.md"
+ )
return analysis_inputs
"""
@@ -675,3 +679,74 @@ rule panacus_stats:
-a {params.apppath} \
-t {threads}
"""
+
+rule create_pan1c_report_fig:
+ # Produces a markdown report figure of chromosomes graphs
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
+ contigfig="output/chr.contig/{chromosome}.contig.png",
+ output:
+ odgifig=temp("tmp/{chromosome}.odgi.png"),
+ namefig=temp("tmp/{chromosome}.name.png"),
+ reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
+ threads: 4
+ params:
+ apppath=config['app.path']
+ shell:
+ """
+ ## Odgi 1D viz
+ apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.odgifig} -x 2000 -a 150 -b -H -t {threads} -P
+
+ ## Getting legend from contig figure
+ convert {input.contigfig} -crop 770x+0+0 +repage {output.namefig}
+
+ odgheight=$(identify -ping -format '%h' {output.odgifig})
+ ctgheight=$(identify -ping -format '%h' {input.contigfig})
+
+ combinedheight=$(($odgheight+$ctgheight))
+
+ echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
+
+ ## Creating empty canvas ad adding other figures to it
+ convert -size "2770x$combinedheight" xc:white {output.reportfig}
+ composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
+ composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
+ composite -geometry "+770+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
+ """
+
+rule create_pan1c_report:
+ # Produces a markdown report of chromosomes graphs
+ input:
+ figs=expand("output/"+config['name']+".{chromosome}.report.fig.png", chromsome=CHRLIST),
+ genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ output:
+ reportfig="output/pan1c."+config['name']+".report.md"
+ threads: 4
+ params:
+ apppath=config['app.path']
+ run:
+ shell("touch {output.reportfig}")
+
+ # Adding General stats
+ shell("echo '# General stats' >> {output.reportfig}")
+ shell("cat {input.genstats} | tr '\\t' ',' | csv2md >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding Path stats
+ shell("echo '# Path stats' >> {output.reportfig}")
+ shell("cat {input.pathstats} | tr '\\t' ',' | csv2md >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding chromosomes figures
+ input.figs.sort()
+
+ shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
+ for fig in input.figs:
+ basename=os.path.basename(fig)
+ chr_name=basename.split('.')[2]
+
+ shell("echo '## {chr_name}' >> {output.reportfig}")
+ shell("echo '[{basename}]({basename}) >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
\ No newline at end of file
diff --git a/config.yaml b/config.yaml
index 05de181..3c09fb6 100644
--- a/config.yaml
+++ b/config.yaml
@@ -16,7 +16,7 @@ wfmash.secondary: '-k 19 -H 0.001 -X'
seqwish.params: '-B 10000000 -k 19 -f 0'
# Odgi 1D and path coverage viz parameters
-odgi.1Dviz.params: '-x 2000 -a 150 -b -H'
+odgi.1Dviz.params: '-x 2000 -a 150 -b'
odgi.pcov.params: '-x 2000 -a 150 -O'
## Optional parts of the workflow
@@ -29,3 +29,5 @@ get_PAV: 'False'
# Computes SyRI figures for haplotypes
#get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference
+# Creating final report
+create_report: 'True'
--
GitLab
From 875288343c1b253f03f557d8621538cc915870e0 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 14:56:27 +0200
Subject: [PATCH 07/86] Fixed CICD
---
.gitlab-ci.yml | 2 +-
example/config_CICD.yaml | 2 ++
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 085078b..828b4de 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -14,7 +14,7 @@ shallow_run_workflow:
## Downloading apps
- mkdir appimgs
#- apptainer build apps/pggb.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/pggb:latest
- - apptainer build appimgs/snakebox.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangratools/snakebox:latest
+ - apptainer pull appimgs/snakebox.sif oras://registry.forgemia.inra.fr/alexis.mergez/pan1capps/pan1cbox:latest
#- apptainer build apps/pytools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pytools:latest
#- apptainer build apps/PanGeTools.sif oras://registry.forgemia.inra.fr/alexis.mergez/pangetools/pangetools:latest
diff --git a/example/config_CICD.yaml b/example/config_CICD.yaml
index 4a415bf..648e686 100644
--- a/example/config_CICD.yaml
+++ b/example/config_CICD.yaml
@@ -29,3 +29,5 @@ get_PAV: 'False'
# Computes SyRI figures for haplotypes
#get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference
+# Creating final report
+create_report: 'True'
--
GitLab
From 2e0935dd2bb68ffbfc68d34666398f8a450caadc Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:00:41 +0200
Subject: [PATCH 08/86] Typo
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 1a7dae4..b7ef24c 100644
--- a/Snakefile
+++ b/Snakefile
@@ -718,7 +718,7 @@ rule create_pan1c_report_fig:
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
input:
- figs=expand("output/"+config['name']+".{chromosome}.report.fig.png", chromsome=CHRLIST),
+ figs=expand("output/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
output:
--
GitLab
From 78c38921c6359962b3d4d6fa00c38c5ac2eb1b6e Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:02:22 +0200
Subject: [PATCH 09/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index b7ef24c..dd513de 100644
--- a/Snakefile
+++ b/Snakefile
@@ -718,7 +718,7 @@ rule create_pan1c_report_fig:
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
input:
- figs=expand("output/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
+ figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
output:
--
GitLab
From bc138d4fd351c090782bb7211062993326dea0a9 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:15:37 +0200
Subject: [PATCH 10/86] Update Snakefile
---
Snakefile | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index dd513de..62344de 100644
--- a/Snakefile
+++ b/Snakefile
@@ -740,10 +740,11 @@ rule create_pan1c_report:
shell("echo '' >> {output.reportfig}")
# Adding chromosomes figures
- input.figs.sort()
+ fig_list = input.figs
+ fig_list.sort()
shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
- for fig in input.figs:
+ for fig in fig_list:
basename=os.path.basename(fig)
chr_name=basename.split('.')[2]
--
GitLab
From 3e28e9b491f01d9b6fe023204ff120c7208057a7 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:18:39 +0200
Subject: [PATCH 11/86] Update Snakefile
---
Snakefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 62344de..289186a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -740,7 +740,8 @@ rule create_pan1c_report:
shell("echo '' >> {output.reportfig}")
# Adding chromosomes figures
- fig_list = input.figs
+ fig_list = [fig for fig in input.figs]
+ print(fig_list)
fig_list.sort()
shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
--
GitLab
From 35f8cb8bf9d1f07fea917c505ec5cf1cae157e28 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:22:57 +0200
Subject: [PATCH 12/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 289186a..782e219 100644
--- a/Snakefile
+++ b/Snakefile
@@ -750,5 +750,5 @@ rule create_pan1c_report:
chr_name=basename.split('.')[2]
shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '[{basename}]({basename}) >> {output.reportfig}")
+ shell("echo '[{basename}]({basename})' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
\ No newline at end of file
--
GitLab
From 4ba2d57f4518d3d88fed8302c5e1dffd3974358b Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:27:51 +0200
Subject: [PATCH 13/86] Update Snakefile
---
Snakefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index 782e219..6d348d0 100644
--- a/Snakefile
+++ b/Snakefile
@@ -731,12 +731,12 @@ rule create_pan1c_report:
# Adding General stats
shell("echo '# General stats' >> {output.reportfig}")
- shell("cat {input.genstats} | tr '\\t' ',' | csv2md >> {output.reportfig}")
+ shell("cat {input.genstats} | csv2md -d'\\t' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
# Adding Path stats
shell("echo '# Path stats' >> {output.reportfig}")
- shell("cat {input.pathstats} | tr '\\t' ',' | csv2md >> {output.reportfig}")
+ shell("cat {input.pathstats} | csv2md -d'\\t' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
# Adding chromosomes figures
@@ -750,5 +750,5 @@ rule create_pan1c_report:
chr_name=basename.split('.')[2]
shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '[{basename}]({basename})' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
\ No newline at end of file
--
GitLab
From 7ff03996368e37a17a428c3d49e03a3bc675d2dc Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:30:10 +0200
Subject: [PATCH 14/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 6d348d0..b84a8fd 100644
--- a/Snakefile
+++ b/Snakefile
@@ -731,12 +731,12 @@ rule create_pan1c_report:
# Adding General stats
shell("echo '# General stats' >> {output.reportfig}")
- shell("cat {input.genstats} | csv2md -d'\\t' >> {output.reportfig}")
+ shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
# Adding Path stats
shell("echo '# Path stats' >> {output.reportfig}")
- shell("cat {input.pathstats} | csv2md -d'\\t' >> {output.reportfig}")
+ shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
# Adding chromosomes figures
--
GitLab
From aff2e1cbba4192bb58ddea8349e8f38ab3df1128 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:38:18 +0200
Subject: [PATCH 15/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index b84a8fd..479ddc7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -747,7 +747,7 @@ rule create_pan1c_report:
shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
for fig in fig_list:
basename=os.path.basename(fig)
- chr_name=basename.split('.')[2]
+ chr_name=basename.split('.')[1]
shell("echo '## {chr_name}' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
--
GitLab
From 0d907efba1faeeb1635e07d2ac92be5f13d3d3ce Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 15:42:06 +0200
Subject: [PATCH 16/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 479ddc7..e8acceb 100644
--- a/Snakefile
+++ b/Snakefile
@@ -750,5 +750,5 @@ rule create_pan1c_report:
chr_name=basename.split('.')[1]
shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
shell("echo '' >> {output.reportfig}")
\ No newline at end of file
--
GitLab
From 9a42d8fb2f2c634758cdf1720619e02cb2584e3a Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 16:39:01 +0200
Subject: [PATCH 17/86] Better figures
---
Snakefile | 11 +++++++----
scripts/contig_position.R | 10 +++++-----
2 files changed, 12 insertions(+), 9 deletions(-)
diff --git a/Snakefile b/Snakefile
index e8acceb..4fc3014 100644
--- a/Snakefile
+++ b/Snakefile
@@ -189,7 +189,7 @@ rule contig_position:
#cat $base/{wildcards.chromosome}.gff
- awk '{{a++; if ((a/2)==int(a/2)){{b="gneg"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
+ awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
> $base/{wildcards.chromosome}.bands
@@ -696,10 +696,10 @@ rule create_pan1c_report_fig:
"""
## Odgi 1D viz
apptainer run --app odgi {params.apppath}/PanGeTools.sif \
- viz -i {input.graph} -o {output.odgifig} -x 2000 -a 150 -b -H -t {threads} -P
+ viz -i {input.graph} -o {output.odgifig} -x 2500 -a 100 -b -H -t {threads} -P
## Getting legend from contig figure
- convert {input.contigfig} -crop 770x+0+0 +repage {output.namefig}
+ convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
odgheight=$(identify -ping -format '%h' {output.odgifig})
ctgheight=$(identify -ping -format '%h' {input.contigfig})
@@ -709,7 +709,7 @@ rule create_pan1c_report_fig:
echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
## Creating empty canvas ad adding other figures to it
- convert -size "2770x$combinedheight" xc:white {output.reportfig}
+ convert -size "2800x$combinedheight" xc:white {output.reportfig}
composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
composite -geometry "+770+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
@@ -729,6 +729,9 @@ rule create_pan1c_report:
run:
shell("touch {output.reportfig}")
+ # Adding Summary
+ ## To Do
+
# Adding General stats
shell("echo '# General stats' >> {output.reportfig}")
shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index d367beb..8d4f5e4 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -34,19 +34,19 @@ my.cytobands <- toGRanges(x)
# Creating figure
# Customizing figure parameters : see https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html
pp <- getDefaultPlotParams(plot.type=1)
-pp$ideogramheight <- 100
-pp$data1outmargin <- 25
-pp$data2outmargin <- 25
+pp$ideogramheight <- 80
+pp$data1outmargin <- 10
+pp$data2outmargin <- 10
pp$data1inmargin <- 0
pp$data2inmargin <- 0
-pp$leftmargin <- 0.28
+pp$leftmargin <- 0.24
pp$rightmargin <- 0
pp$topmargin <- 0
pp$bottommargin <- 0
pp$data1height <- 0
pp$data2height <- 0
-png(opt$out, width=2780, height=(nChr*150), pointsize=6, res=300, antialias = "none")
+png(opt$out, width=3300, height=(nChr*100), pointsize=6, res=300, antialias = "none")
kp <- plotKaryotype(genome=my.genome, cytobands=my.cytobands, plot.params=pp, chromosomes="all")
kp <- kpAddBaseNumbers(kp, cex=0.6, tick.dist=5000000)
dev.off()
\ No newline at end of file
--
GitLab
From 1593a417d6709739197f7f9088aa2c03483749e9 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 17:01:08 +0200
Subject: [PATCH 18/86] Lexographical sorting of chromosomes
---
scripts/chrInputStats.py | 3 +++
scripts/chrStatsAggregation.py | 2 ++
scripts/coreStats.py | 5 +++++
3 files changed, 10 insertions(+)
diff --git a/scripts/chrInputStats.py b/scripts/chrInputStats.py
index 8b3015b..85d3d26 100644
--- a/scripts/chrInputStats.py
+++ b/scripts/chrInputStats.py
@@ -55,6 +55,9 @@ Sequence dictionnary :
"""
seqDict = {}
+# Sorting
+args.fastafiles.sort()
+
# Parsing fasta files
for filename in args.fastafiles:
diff --git a/scripts/chrStatsAggregation.py b/scripts/chrStatsAggregation.py
index 3ac2b10..404549e 100644
--- a/scripts/chrStatsAggregation.py
+++ b/scripts/chrStatsAggregation.py
@@ -43,6 +43,8 @@ args = arg_parser.parse_args()
## Main script
# Getting the list of stats files
fileList = [k for k in os.listdir(args.inputDir) if k[-3:] == "tsv"]
+# Sorting
+fileList.sort()
stats = {
"general": [],
diff --git a/scripts/coreStats.py b/scripts/coreStats.py
index 91e693f..db0991c 100644
--- a/scripts/coreStats.py
+++ b/scripts/coreStats.py
@@ -72,6 +72,10 @@ arg_parser.add_argument(
)
args = arg_parser.parse_args()
+# Sorting
+args.chrGraphStatsFiles.sort()
+args.chrInputStatsFiles.sort()
+
## Toolbox
def getRegEquation(x, y):
(slope, intercept), ssr, _1, _2, _3 = np.polyfit(x, y, 1, full = True)
@@ -89,6 +93,7 @@ PGGBsteps = [] # Storing PGGB steps name
# Iterating through all pggb time stats
TimeStatsList = [os.path.join(args.pggbStats, file) for file in os.listdir(args.pggbStats) if file.split('.')[-2] == "time"]
+TimeStatsList.sort()
print(TimeStatsList)
for pggbStats in TimeStatsList:
--
GitLab
From 4330f3e27a76cd44f4a135ec9b6a184154c20c2a Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 17:14:13 +0200
Subject: [PATCH 19/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 4fc3014..8b778d7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -709,10 +709,10 @@ rule create_pan1c_report_fig:
echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
## Creating empty canvas ad adding other figures to it
- convert -size "2800x$combinedheight" xc:white {output.reportfig}
+ convert -size "3300x$combinedheight" xc:white {output.reportfig}
composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
- composite -geometry "+770+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
+ composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
"""
rule create_pan1c_report:
--
GitLab
From 1dbe14c244827c8725481f16fb4f8dc623cd4e8e Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Fri, 21 Jun 2024 18:54:02 +0200
Subject: [PATCH 20/86] Updated report figures
---
Snakefile | 2 +-
scripts/contig_position.R | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/Snakefile b/Snakefile
index 8b778d7..5b3598a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -696,7 +696,7 @@ rule create_pan1c_report_fig:
"""
## Odgi 1D viz
apptainer run --app odgi {params.apppath}/PanGeTools.sif \
- viz -i {input.graph} -o {output.odgifig} -x 2500 -a 100 -b -H -t {threads} -P
+ viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
## Getting legend from contig figure
convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 8d4f5e4..01f9f93 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -34,9 +34,9 @@ my.cytobands <- toGRanges(x)
# Creating figure
# Customizing figure parameters : see https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html
pp <- getDefaultPlotParams(plot.type=1)
-pp$ideogramheight <- 80
-pp$data1outmargin <- 10
-pp$data2outmargin <- 10
+pp$ideogramheight <- 50
+pp$data1outmargin <- 15
+pp$data2outmargin <- 15
pp$data1inmargin <- 0
pp$data2inmargin <- 0
pp$leftmargin <- 0.24
@@ -46,7 +46,7 @@ pp$bottommargin <- 0
pp$data1height <- 0
pp$data2height <- 0
-png(opt$out, width=3300, height=(nChr*100), pointsize=6, res=300, antialias = "none")
+png(opt$out, width=3300, height=(nChr*80), pointsize=6, res=300, antialias = "none")
kp <- plotKaryotype(genome=my.genome, cytobands=my.cytobands, plot.params=pp, chromosomes="all")
kp <- kpAddBaseNumbers(kp, cex=0.6, tick.dist=5000000)
dev.off()
\ No newline at end of file
--
GitLab
From f9f272511a61bb99a489e2b6a38b869acf78dcc8 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 08:14:08 +0200
Subject: [PATCH 21/86] Update getSyriFigs.sh
Renaming chromosomes based on reference to prevent SyRI from matching chromosomes and crashing
---
scripts/getSyriFigs.sh | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 3f3c7ff..ab2f0d1 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -45,6 +45,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Setting filepaths for later
bamFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).bam"
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
+ hapID=$(basename ${asmList[i + 1]} .fa.gz | sed 's/.hap/#/')
+ refID=$(basename ${asmList[i]} .fa.gz | sed 's/.hap/#/')
# Adding the output syri file to the array
syriFileList+=($syriFile)
@@ -53,6 +55,9 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
apptainer run $appdir/pan1c-env.sif python scripts/syri_pruning.py \
-r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir
+ # Renaming chromosomes with same ids as the reference
+ sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
+
#Â Minimap2 genome vs genome alignment
apptainer run --app minimap2 $appdir/PanGeTools.sif \
-a -x asm5 -c --eqx \
--
GitLab
From 856620b5e6de2eb84fb7b7bcfeab53c661ec64c7 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 08:14:52 +0200
Subject: [PATCH 22/86] Update getPanacusHG.sh
Not grouping samples anymore
---
scripts/getPanacusHG.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getPanacusHG.sh b/scripts/getPanacusHG.sh
index 7f3ddb9..d26dda3 100755
--- a/scripts/getPanacusHG.sh
+++ b/scripts/getPanacusHG.sh
@@ -35,4 +35,4 @@ grep '^P' $gfa | cut -f2 | grep -ve "$ref" > ${chrdir}/$chrname.paths.noref.txt
# Running Panacus
echo "[getPanacusHG::panacus] Running on ${gfa}"
apptainer run --app panacus $appdir/PanGeTools.sif histgrowth \
- -t $threads -l 1,2,1,1,1 -q 0,0,1,0.5,0.1 -S -a -s ${chrdir}/$chrname.paths.noref.txt -c all -o html $gfa > ${output}
+ -t $threads -l 1,2,1,1,1 -q 0,0,1,0.5,0.1 -a -s ${chrdir}/$chrname.paths.noref.txt -c all -o html $gfa > ${output}
--
GitLab
From cdd042f90b8e40012452b2d60e68b677f2d56c70 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 09:08:03 +0200
Subject: [PATCH 23/86] Update Snakefile
Better RagTag fasta emptyness check
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 5b3598a..c7683a2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -125,8 +125,8 @@ rule ragtag_scaffolding:
-q {input.fa} \
-o {output.fa}
- if [ ! -s {output.fa} ]; then
- echo "Empty fasta"
+ if [[ -z $(grep '[^[:space:]]' {output.fa}) ]] ; then
+ echo "Error : Empty final fasta"
exit 1
fi
"""
--
GitLab
From 6d6ecbef184438bd350a6eccf790577458a5df48 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 09:09:06 +0200
Subject: [PATCH 24/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index c7683a2..6752afc 100644
--- a/Snakefile
+++ b/Snakefile
@@ -125,7 +125,7 @@ rule ragtag_scaffolding:
-q {input.fa} \
-o {output.fa}
- if [[ -z $(grep '[^[:space:]]' {output.fa}) ]] ; then
+ if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
echo "Error : Empty final fasta"
exit 1
fi
--
GitLab
From 2d0eb5bdccf2bf161269dca6bddfd1f72510a219 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 09:20:29 +0200
Subject: [PATCH 25/86] Update contig_position.R
---
scripts/contig_position.R | 51 +++++++++++++++++++++++++++++----------
1 file changed, 38 insertions(+), 13 deletions(-)
diff --git a/scripts/contig_position.R b/scripts/contig_position.R
index 01f9f93..b0eeb0a 100644
--- a/scripts/contig_position.R
+++ b/scripts/contig_position.R
@@ -33,20 +33,45 @@ my.cytobands <- toGRanges(x)
# Creating figure
# Customizing figure parameters : see https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotParams/PlotParams.html
+
pp <- getDefaultPlotParams(plot.type=1)
-pp$ideogramheight <- 50
-pp$data1outmargin <- 15
-pp$data2outmargin <- 15
-pp$data1inmargin <- 0
-pp$data2inmargin <- 0
-pp$leftmargin <- 0.24
-pp$rightmargin <- 0
-pp$topmargin <- 0
-pp$bottommargin <- 0
-pp$data1height <- 0
-pp$data2height <- 0
-
-png(opt$out, width=3300, height=(nChr*80), pointsize=6, res=300, antialias = "none")
+
+if (nChr >= 4){
+
+ pp$ideogramheight <- 50
+ pp$data1outmargin <- 15
+ pp$data2outmargin <- 15
+ pp$data1inmargin <- 0
+ pp$data2inmargin <- 0
+ pp$leftmargin <- 0.24
+ pp$rightmargin <- 0
+ pp$topmargin <- 0
+ pp$bottommargin <- 0
+ pp$data1height <- 0
+ pp$data2height <- 0
+
+ png(opt$out, width=3300, height=(nChr*80), pointsize=6, res=300, antialias = "none")
+
+} else {
+ # Too low chromosomes cause crash in par handler.
+ pp$ideogramheight <- 50
+ pp$data1outmargin <- 15
+ pp$data2outmargin <- 15
+ pp$data1inmargin <- 0
+ pp$data2inmargin <- 0
+ pp$leftmargin <- 0.24
+ pp$rightmargin <- 0
+ pp$topmargin <- 0.5
+ pp$bottommargin <- 0
+ pp$data1height <- 0
+ pp$data2height <- 0
+
+ png(opt$out, width=3300, height=(nChr*80*2), pointsize=6, res=300, antialias = "none")
+
+}
+
+
+
kp <- plotKaryotype(genome=my.genome, cytobands=my.cytobands, plot.params=pp, chromosomes="all")
kp <- kpAddBaseNumbers(kp, cex=0.6, tick.dist=5000000)
dev.off()
\ No newline at end of file
--
GitLab
From b8a30f4d9460051f4b68b4cc0987995fb3b6fb84 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 10:21:01 +0200
Subject: [PATCH 26/86] Update Snakefile
Allowing retries for SyRI
---
Snakefile | 1 +
1 file changed, 1 insertion(+)
diff --git a/Snakefile b/Snakefile
index 6752afc..e0c3e0d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -266,6 +266,7 @@ rule create_sglAsm_syri_fig:
fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
wrkdir=directory('data/asm.syri/{haplotype}')
threads: 4
+ retries: 1
resources:
mem_gb=48
params:
--
GitLab
From 0e16a0448879356cb7405f49db2390fb4686b469 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 13:30:42 +0200
Subject: [PATCH 27/86] Update Snakefile
---
Snakefile | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index e0c3e0d..839292a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -125,10 +125,10 @@ rule ragtag_scaffolding:
-q {input.fa} \
-o {output.fa}
- if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
- echo "Error : Empty final fasta"
- exit 1
- fi
+ #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
+ # echo "Error : Empty final fasta"
+ # exit 1
+ #fi
"""
rule quast_stats:
--
GitLab
From a9ed84f4e4f8f1350c226e4744821f0c1214384c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 15:01:25 +0200
Subject: [PATCH 28/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index ab2f0d1..0b02e0d 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -47,6 +47,9 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
hapID=$(basename ${asmList[i + 1]} .fa.gz | sed 's/.hap/#/')
refID=$(basename ${asmList[i]} .fa.gz | sed 's/.hap/#/')
+
+ # Debug
+ echo -e "[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID"
# Adding the output syri file to the array
syriFileList+=($syriFile)
@@ -65,7 +68,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
-t $threads > $wrkdir/$bamFile.sam
apptainer run --app samtools $appdir/PanGeTools.sif sort -O BAM -@ $threads $wrkdir/$bamFile.sam > $wrkdir/$bamFile
- rm $wrkdir/$bamFile.sam $wrkdir/*.fa
+ rm $wrkdir/$bamFile.sam
+ #rm $wrkdir/*.fa
# Syri on previous alignment
apptainer run $appdir/pan1c-env.sif \
--
GitLab
From e01c06ad43a3fc80568bf718568fafdb1bf18b0c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 15:41:09 +0200
Subject: [PATCH 29/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 0b02e0d..8f845b9 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -45,8 +45,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Setting filepaths for later
bamFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).bam"
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
- hapID=$(basename ${asmList[i + 1]} .fa.gz | sed 's/.hap/#/')
- refID=$(basename ${asmList[i]} .fa.gz | sed 's/.hap/#/')
+ hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
# Debug
echo -e "[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID"
--
GitLab
From bffc5e642d18f395cbd04c7325cffb58c1041897 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 24 Jun 2024 15:48:31 +0200
Subject: [PATCH 30/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 8f845b9..3baf716 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -45,8 +45,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Setting filepaths for later
bamFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).bam"
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
- hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
- refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ #hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ #refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
# Debug
echo -e "[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID"
@@ -58,8 +58,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
apptainer run $appdir/pan1c-env.sif python scripts/syri_pruning.py \
-r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir
- # Renaming chromosomes with same ids as the reference
- sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
+ # Renaming chromosomes with same ids as the reference (Not working)
+ #sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
#Â Minimap2 genome vs genome alignment
apptainer run --app minimap2 $appdir/PanGeTools.sif \
--
GitLab
From 511e110b6289e05fa0629691b2c3fa557779ae0c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:36:56 +0200
Subject: [PATCH 31/86] Testing moving rules to dedicated files
---
Snakefile | 235 ++++++++++++++++++++++++------------------------
rules/tools.smk | 16 ++++
2 files changed, 133 insertions(+), 118 deletions(-)
create mode 100644 rules/tools.smk
diff --git a/Snakefile b/Snakefile
index 839292a..052810c 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,5 +1,8 @@
configfile: "config.yaml"
+include: "rules/tools.smk"
+
+
## Modules
import os
import numpy as np
@@ -7,15 +10,15 @@ import gzip
import re
"""
-
-Main variables used in the workflow
-
+Main variables used in the workflow ---------------------------------------------------------------
"""
-# Retrieving the list of haplotypes (SAMPLES) in data/haplotypes
+
+# Retrieving the list of haplotypes (SAMPLES) in data/haplotypes.
+# File with .fa extension only will be used. (.fna will not be used)
SAMPLES = np.unique([
- os.path.basename(f).split('.fa')[0]
- for f in os.listdir("data/haplotypes/")
- if re.search(r"\.fa", f)
+ os.path.basename(file).split('.fa')[0]
+ for file in os.listdir("data/haplotypes/")
+ if re.search(r"\.fa", file)
])
# Retrieving the list of haplotypes excluding the reference
@@ -32,9 +35,10 @@ nHAP = len(SAMPLES)
with gzip.open("data/haplotypes/"+config['reference'], "r") as handle:
CHRLIST = [line.decode().split("#")[-1].split('\n')[0] for line in handle.readlines() if line.decode()[0] == ">"]
-# Adjusting the requested outputs according to the config file
+# Adding optionnal output based on config.yaml, using the following function
def which_analysis():
- # Creating a list with default analysis steps (to prevent the function from returning an empty list)
+
+ ## Default analysis
analysis_inputs = [
"output/stats/pan1c."+config['name']+".core.stats.tsv", # core stats
expand("output/panacus.reports/"+config['name']+".{chromosome}.histgrowth.html", chromosome=CHRLIST), # panacus histgrowth
@@ -42,33 +46,32 @@ def which_analysis():
"output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv" # chromosomes graph statistics
]
- # Optionals analysis steps
+ ## Optionals analysis steps
if config["get_PAV"] == "True": # Adding PAV matrix creation
analysis_inputs.append("output/pav.matrices")
- #if config["get_allASM_SyRI"] == "True": # Creating the figure for all assemblies
- # analysis_inputs.append("output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png")
- if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures
+
+ if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures
analysis_inputs.append(
- expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF), # syri for haplotypes
+ expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF),
)
- if config["run_Quast"] == "True": # Running quast on haplotypes
+ if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
"output/quast/Quast.report.html"
)
- if config["get_contig_pos"] == "True": # Contig position in chromosomes figure
+ if config["get_contig_pos"] == "True": # Chromosome decomposition into its contig figure
analysis_inputs.append(
expand("output/chr.contig/{haplotype}.contig.png", haplotype=CHRLIST)
)
- if config["create_report"] == "True": # Create report
- analysis_inputs.append(
- "output/pan1c."+config['name']+".report.md"
- )
- return analysis_inputs
-"""
+ if config["create_report"] == "True": # Creating report (need contig)
+ analysis_inputs.append(
+ "output/pan1c."+config['name']+".report.md"
+ )
-Rules
+ return analysis_inputs
+"""
+Rules -------------------------------------------------------------------------------------------
"""
# Main target rule
rule all:
@@ -77,29 +80,25 @@ rule all:
"output/pan1c."+config['name']+".gfa.metadata", # Metadata for the final (also in top of gfa files as # line)
which_analysis()
-"""
-
-Tool rules
-
-"""
-rule samtools_index:
- # Samtools faidx to index compressed fasta
- input:
- fa="{sample}.fa.gz"
- output:
- "{sample}.fa.gz.fai",
- "{sample}.fa.gz.gzi"
- threads: 1
- params:
- apppath=config["app.path"]
- shell:
- "apptainer run --app samtools {params.apppath}/PanGeTools.sif "
- "faidx {input.fa}"
+# """
+# Tool rules ---------------------------------------------------------------------------------------
+# """
+# rule samtools_index:
+# # Samtools faidx to index compressed fasta
+# input:
+# fa="{sample}.fa.gz"
+# output:
+# "{sample}.fa.gz.fai",
+# "{sample}.fa.gz.gzi"
+# threads: 1
+# params:
+# app_path=config["app.path"]
+# shell:
+# "apptainer run --app samtools {params.app_path}/PanGeTools.sif "
+# "faidx {input.fa}"
"""
-
-Pre-processing section : preparing pggb inputs
-
+Pre-processing section : preparing pggb inputs ---------------------------------------------------
"""
rule ragtag_scaffolding:
# Scaffold input haplotype against the reference to infer chromosome scale sequences
@@ -114,12 +113,12 @@ rule ragtag_scaffolding:
threads: 8
retries: 1
params:
- apppath=config["app.path"]
+ app_path=config["app.path"]
shell:
"""
bash scripts/ragtagChromInfer.sh \
-d $(dirname {output.fa})/{wildcards.haplotype} \
- -a {params.apppath} \
+ -a {params.app_path} \
-t {threads} \
-r {input.ref} \
-q {input.fa} \
@@ -137,14 +136,14 @@ rule quast_stats:
fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
ref="data/haplotypes/"+config['reference']
output:
- report="output/quast/Quast.report.html"
- threads: workflow.cores//2
+ report="output/quast/"+config['name']+".quast.report.html"
+ threads: 8
params:
- apppath=config["app.path"],
- panname=config["name"]
+ app_path=config["app.path"],
+ pan_name=config["name"]
shell:
"""
- apptainer run {params.apppath}/pan1c-env.sif quast.py \
+ apptainer run {params.app_path}/pan1c-env.sif quast.py \
-t {threads} \
-o "$(dirname {output.report})" \
-r {input.ref} \
@@ -156,9 +155,9 @@ rule quast_stats:
{input.fas}
# Compressing temporary files
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} $(dirname {output.report})/contigs_reports/*.fa
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
mv $(dirname {output.report})/report.html {output.report}
@@ -174,7 +173,7 @@ rule contig_position:
outdir=directory("output/chr.contig/{chromosome}")
threads: 1
params:
- apppath=config["app.path"]
+ app_path=config["app.path"]
shell:
"""
mkdir {output.outdir}
@@ -182,7 +181,7 @@ rule contig_position:
hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
# Creating .bands file
- apptainer run {params.apppath}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
-s 5 \
-f {input.fa} \
> $base/{wildcards.chromosome}.gff
@@ -206,7 +205,7 @@ rule contig_position:
#cat $base/{wildcards.chromosome}.tsv
# Creating figure
- apptainer run --app Renv {params.apppath}/pan1c-env.sif Rscript scripts/contig_position.R \
+ apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
-b $base/{wildcards.chromosome}.bands \
-t $base/{wildcards.chromosome}.tsv \
-o {output.fig}
@@ -220,15 +219,15 @@ rule clustering:
expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
threads: workflow.cores
params:
- apppath=config["app.path"],
- panname=config["name"]
+ app_path=config["app.path"],
+ pan_name=config["name"]
shell:
"""
mkdir -p $(dirname {output[0]})
- apptainer run {params.apppath}/pan1c-env.sif python scripts/inputClustering.py \
- --fasta {input} --output $(dirname {output[0]}) --panname {params.panname}
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
+ --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
for file in $(dirname {output[0]})/*.fa; do
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif -@ {threads} $file
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
done
"""
@@ -242,13 +241,13 @@ rule create_allAsm_syri_fig:
wrkdir=directory('data/asm.syri/all')
threads: 8
params:
- apppath=config["app.path"]
+ app_path=config["app.path"]
shell:
"""
mkdir {output.wrkdir}
bash scripts/getSyriFigs.sh \
- -a {params.apppath} \
+ -a {params.app_path} \
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
@@ -270,12 +269,12 @@ rule create_sglAsm_syri_fig:
resources:
mem_gb=48
params:
- apppath=config["app.path"]
+ app_path=config["app.path"]
shell:
"""
mkdir -p {output.wrkdir}
bash scripts/getSyriFigs.sh \
- -a {params.apppath} \
+ -a {params.app_path} \
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
@@ -298,7 +297,7 @@ rule create_pggb_input_syri_fig:
wrkdir=directory('data/chrInput/syri/{chromosome}')
threads: 8
params:
- apppath=config["app.path"],
+ app_path=config["app.path"],
ref=config['reference']
shell:
"""
@@ -318,7 +317,7 @@ rule create_pggb_input_syri_fig:
done
bash scripts/getSyriFigs.sh \
- -a {params.apppath} \
+ -a {params.app_path} \
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
@@ -338,7 +337,7 @@ rule wfmash_on_chr:
aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
threads: 16
params:
- apppath=config['app.path'],
+ app_path=config['app.path'],
segment_length=config['wfmash.segment_length'],
mapping_id=config['wfmash.mapping_id'],
wfmash_sec=config['wfmash.secondary']
@@ -351,7 +350,7 @@ rule wfmash_on_chr:
"""
## Mapping
/usr/bin/time -v -o {log.time_map} \
- apptainer exec {params.apppath}/pggb.sif wfmash \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
-s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
-n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
--tmp-base $(dirname {output.aln}) \
@@ -361,7 +360,7 @@ rule wfmash_on_chr:
## Aligning
/usr/bin/time -v -o {log.time_aln} \
- apptainer exec {params.apppath}/pggb.sif wfmash \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
-s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
-n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
--tmp-base $(dirname {output.aln}) \
@@ -371,10 +370,10 @@ rule wfmash_on_chr:
2> >(tee {log.cmd_aln} >&2)
# Compressing
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} -k {output.mapping}
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} -k {output.aln}
"""
@@ -387,7 +386,7 @@ rule seqwish:
temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
threads: 8
params:
- apppath=config['app.path'],
+ app_path=config['app.path'],
seqwish=config['seqwish.params']
log:
cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
@@ -395,14 +394,14 @@ rule seqwish:
shell:
"""
/usr/bin/time -v -o {log.time} \
- apptainer exec {params.apppath}/pggb.sif seqwish \
+ apptainer exec {params.app_path}/pggb.sif seqwish \
-s {input.fa} -p {input.aln} -g {output} \
{params.seqwish} -t {threads} \
--temp-dir $(dirname {output}) -P 2>&1 | \
tee {log.cmd}
# Compressing
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} -k {output}
"""
@@ -415,18 +414,18 @@ rule gfaffix_on_chr:
transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
threads: 1
params:
- apppath=config['app.path']
+ app_path=config['app.path']
log:
time="logs/pggb/{chromosome}.gfaffix.time.log"
shell:
"""
/usr/bin/time -v -o {log.time} \
- apptainer exec {params.apppath}/pggb.sif gfaffix \
+ apptainer exec {params.app_path}/pggb.sif gfaffix \
{input} -o {output.gfa} -t {output.transform} \
> /dev/null
# Compressing
- apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} -k {output.gfa}
"""
@@ -438,7 +437,7 @@ rule odgi_postprocessing:
gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
threads: 8
params:
- apppath=config['app.path']
+ app_path=config['app.path']
log:
cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
time_build="logs/pggb/{chromosome}.odgi_build.time.log",
@@ -454,26 +453,26 @@ rule odgi_postprocessing:
## Converting to odgi format and optimizing namespace
/usr/bin/time -v -o {log.time_build} \
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
tee {log.cmd_build}
## Unchoping the nodes (merges unitigs into single nodes)
/usr/bin/time -v -o {log.time_unchop} \
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
tee {log.cmd_unchop}
## Sorting the nodes
/usr/bin/time -v -o {log.time_sort} \
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
-i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
tee {log.cmd_sort}
## Exporting to gfa
/usr/bin/time -v -o {log.time_view} \
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
view -i $OGfile.unchoped.sorted.og -g \
1> {output.gfa} \
2> >(tee {log.cmd_view} >&2)
@@ -483,12 +482,12 @@ rule odgi_postprocessing:
## Adding metadata
python scripts/getTags.py \
- --appdir {params.apppath} --config-file config.yaml \
+ --appdir {params.app_path} --config-file config.yaml \
> "$(dirname {input})/metadata.txt"
sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
# Compressing
- # apptainer run --app bgzip {params.apppath}/PanGeTools.sif \
+ # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
# -@ {threads} -k {output.gfa}
"""
@@ -513,12 +512,12 @@ rule graph_squeeze:
"output/pan1c."+config['name']+".gfa"
threads: 16
params:
- apppath=config['app.path']
+ app_path=config['app.path']
shell:
"""
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
view -t {threads} -P -i {output}.og -g > {output}
rm {output}.og
"""
@@ -532,13 +531,13 @@ rule graph_stats:
pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
threads: 4
params:
- apppath=config['app.path'],
- panname=config['name']
+ app_path=config['app.path'],
+ pan_name=config['name']
shell:
"""
- apptainer run --app gfastats {params.apppath}/PanGeTools.sif \
+ apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
-g {input.graph} -P \
- -o $(dirname {output.genstats})/{params.panname}.{wildcards.chromosome} \
+ -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
-t {threads}
"""
@@ -551,17 +550,17 @@ rule graph_figs:
pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
threads: 4
params:
- apppath=config['app.path'],
+ app_path=config['app.path'],
oneDviz=config['odgi.1Dviz.params'],
pcov=config['odgi.pcov.params']
shell:
"""
## 1D viz
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
## Pcov viz
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
"""
@@ -573,13 +572,13 @@ rule aggregate_graphs_stats:
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
params:
- apppath=config['app.path'],
- panname=config['name']
+ app_path=config['app.path'],
+ pan_name=config['name']
shell:
"""
- apptainer run {params.apppath}/pan1c-env.sif python scripts/chrStatsAggregation.py \
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
--input $(dirname {input[0]}) --outputGeneral {output.genstats} \
- --outputPaths {output.pathstats} --panname {params.panname}
+ --outputPaths {output.pathstats} --panname {params.pan_name}
"""
rule final_graph_tagging:
@@ -590,12 +589,12 @@ rule final_graph_tagging:
"output/pan1c."+config['name']+".gfa.metadata"
threads: 1
params:
- apppath=config['app.path'],
- panname=config['name']
+ app_path=config['app.path'],
+ pan_name=config['name']
shell:
"""
python scripts/getTags.py \
- --appdir {params.apppath} --config-file config.yaml > {output}
+ --appdir {params.app_path} --config-file config.yaml > {output}
sed -i '/^H/r {output}' {input.graph}
"""
@@ -606,12 +605,12 @@ rule pggb_input_stats:
output:
"output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
params:
- apppath=config['app.path'],
- panname=config['name']
+ app_path=config['app.path'],
+ pan_name=config['name']
shell:
"""
- apptainer run {params.apppath}/pan1c-env.sif python scripts/chrInputStats.py \
- -f data/chrInputs/*.fa.gz -o {output} -p {params.panname}
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
+ -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
"""
rule core_statistics:
@@ -623,14 +622,14 @@ rule core_statistics:
tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
dir=directory("output/pggb.usage.figs")
params:
- apppath=config['app.path'],
- panname=config['name']
+ app_path=config['app.path'],
+ pan_name=config['name']
shell:
"""
mkdir -p {output.dir}
- apptainer run {params.apppath}/pan1c-env.sif python scripts/coreStats.py \
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
--pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
- --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.panname}
+ --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
"""
"""
@@ -649,7 +648,7 @@ rule get_pav:
directory("output/pav.matrices")
threads: 16
params:
- apppath=config['app.path']
+ app_path=config['app.path']
run:
shell("mkdir {output}")
# Getting the list of graphs
@@ -657,7 +656,7 @@ rule get_pav:
graphList = [graph.rstrip("\n") for graph in handle.readlines()]
# Iterating over graphs
for graph in graphList:
- shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.apppath} -t {threads}")
+ shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
rule panacus_stats:
# Produces panacus reports for a chromosome graph
@@ -666,8 +665,8 @@ rule panacus_stats:
output:
html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
params:
- apppath=config['app.path'],
- panname=config['name'],
+ app_path=config['app.path'],
+ pan_name=config['name'],
refname=config['reference']
threads: 8
shell:
@@ -677,7 +676,7 @@ rule panacus_stats:
-r $(basename {params.refname} .fa.gz) \
-d data/chrGraphs/{wildcards.chromosome} \
-o {output.html} \
- -a {params.apppath} \
+ -a {params.app_path} \
-t {threads}
"""
@@ -692,11 +691,11 @@ rule create_pan1c_report_fig:
reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
threads: 4
params:
- apppath=config['app.path']
+ app_path=config['app.path']
shell:
"""
## Odgi 1D viz
- apptainer run --app odgi {params.apppath}/PanGeTools.sif \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
## Getting legend from contig figure
@@ -726,7 +725,7 @@ rule create_pan1c_report:
reportfig="output/pan1c."+config['name']+".report.md"
threads: 4
params:
- apppath=config['app.path']
+ app_path=config['app.path']
run:
shell("touch {output.reportfig}")
diff --git a/rules/tools.smk b/rules/tools.smk
new file mode 100644
index 0000000..7528154
--- /dev/null
+++ b/rules/tools.smk
@@ -0,0 +1,16 @@
+"""
+Tool rules ---------------------------------------------------------------------------------------
+"""
+rule samtools_index:
+ # Samtools faidx to index compressed fasta
+ input:
+ fa="{sample}.fa.gz"
+ output:
+ "{sample}.fa.gz.fai",
+ "{sample}.fa.gz.gzi"
+ threads: 1
+ params:
+ app_path=config["app.path"]
+ shell:
+ "apptainer run --app samtools {params.app_path}/PanGeTools.sif "
+ "faidx {input.fa}"
\ No newline at end of file
--
GitLab
From 715361a591f020f8b5bf3c14378ea8def17685a5 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:40:18 +0200
Subject: [PATCH 32/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 052810c..a57f18d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -56,7 +56,7 @@ def which_analysis():
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
- "output/quast/Quast.report.html"
+ "output/quast/"+config['name']+"Quast.report.html"
)
if config["get_contig_pos"] == "True": # Chromosome decomposition into its contig figure
analysis_inputs.append(
--
GitLab
From 8b78a0262b616a724a1b13074dcab1ac45515c0d Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:41:04 +0200
Subject: [PATCH 33/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index a57f18d..40bba47 100644
--- a/Snakefile
+++ b/Snakefile
@@ -56,7 +56,7 @@ def which_analysis():
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
- "output/quast/"+config['name']+"Quast.report.html"
+ "output/quast/"+config['name']+".quast.report.html"
)
if config["get_contig_pos"] == "True": # Chromosome decomposition into its contig figure
analysis_inputs.append(
--
GitLab
From 32673952cdc1dc79cf5c9e751c2768826906b767 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:47:15 +0200
Subject: [PATCH 34/86] Moved rules to dedicated SMK files
---
Snakefile | 1294 +++++++++++++++++++-------------------
rules/core.smk | 346 ++++++++++
rules/post-analysis.smk | 118 ++++
rules/pre-processing.smk | 185 ++++++
4 files changed, 1295 insertions(+), 648 deletions(-)
create mode 100644 rules/core.smk
create mode 100644 rules/post-analysis.smk
create mode 100644 rules/pre-processing.smk
diff --git a/Snakefile b/Snakefile
index 40bba47..0577e00 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,7 +1,9 @@
configfile: "config.yaml"
include: "rules/tools.smk"
-
+include: "rules/pre-processing.smk"
+include: "rules/core.smk"
+include: "rules/post-analysis.smk"
## Modules
import os
@@ -97,661 +99,657 @@ rule all:
# "apptainer run --app samtools {params.app_path}/PanGeTools.sif "
# "faidx {input.fa}"
-"""
-Pre-processing section : preparing pggb inputs ---------------------------------------------------
-"""
-rule ragtag_scaffolding:
- # Scaffold input haplotype against the reference to infer chromosome scale sequences
- input:
- ref="data/haplotypes/"+config['reference'],
- reffai="data/haplotypes/"+config['reference']+".fai",
- refgzi="data/haplotypes/"+config['reference']+".gzi",
- fa="data/haplotypes/{haplotype}.fa.gz"
- output:
- fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
- tar="data/hap.ragtagged/{haplotype}.tar.gz"
- threads: 8
- retries: 1
- params:
- app_path=config["app.path"]
- shell:
- """
- bash scripts/ragtagChromInfer.sh \
- -d $(dirname {output.fa})/{wildcards.haplotype} \
- -a {params.app_path} \
- -t {threads} \
- -r {input.ref} \
- -q {input.fa} \
- -o {output.fa}
-
- #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
- # echo "Error : Empty final fasta"
- # exit 1
- #fi
- """
-
-rule quast_stats:
- # Run Quast on ragtagged genomes
- input:
- fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
- ref="data/haplotypes/"+config['reference']
- output:
- report="output/quast/"+config['name']+".quast.report.html"
- threads: 8
- params:
- app_path=config["app.path"],
- pan_name=config["name"]
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif quast.py \
- -t {threads} \
- -o "$(dirname {output.report})" \
- -r {input.ref} \
- --plots-format png \
- --no-read-stats \
- --no-icarus \
- -s \
- --large \
- {input.fas}
-
- # Compressing temporary files
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
-
- mv $(dirname {output.report})/report.html {output.report}
- """
-
-rule contig_position:
- # Produce figures with contig positions
- input:
- fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
- fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
- output:
- fig="output/chr.contig/{chromosome}.contig.png",
- outdir=directory("output/chr.contig/{chromosome}")
- threads: 1
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir {output.outdir}
- base="{output.outdir}"
- hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
+# """
+# Pre-processing section : preparing pggb inputs ---------------------------------------------------
+# """
+# rule ragtag_scaffolding:
+# # Scaffold input haplotype against the reference to infer chromosome scale sequences
+# input:
+# ref="data/haplotypes/"+config['reference'],
+# reffai="data/haplotypes/"+config['reference']+".fai",
+# refgzi="data/haplotypes/"+config['reference']+".gzi",
+# fa="data/haplotypes/{haplotype}.fa.gz"
+# output:
+# fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
+# tar="data/hap.ragtagged/{haplotype}.tar.gz"
+# threads: 8
+# retries: 1
+# params:
+# app_path=config["app.path"]
+# shell:
+# """
+# bash scripts/ragtagChromInfer.sh \
+# -d $(dirname {output.fa})/{wildcards.haplotype} \
+# -a {params.app_path} \
+# -t {threads} \
+# -r {input.ref} \
+# -q {input.fa} \
+# -o {output.fa}
+
+# #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
+# # echo "Error : Empty final fasta"
+# # exit 1
+# #fi
+# """
+
+# rule quast_stats:
+# # Run Quast on ragtagged genomes
+# input:
+# fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
+# ref="data/haplotypes/"+config['reference']
+# output:
+# report="output/quast/"+config['name']+".quast.report.html"
+# threads: 8
+# params:
+# app_path=config["app.path"],
+# pan_name=config["name"]
+# shell:
+# """
+# apptainer run {params.app_path}/pan1c-env.sif quast.py \
+# -t {threads} \
+# -o "$(dirname {output.report})" \
+# -r {input.ref} \
+# --plots-format png \
+# --no-read-stats \
+# --no-icarus \
+# -s \
+# --large \
+# {input.fas}
+
+# # Compressing temporary files
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
+
+# mv $(dirname {output.report})/report.html {output.report}
+# """
+
+# rule contig_position:
+# # Produce figures with contig positions
+# input:
+# fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
+# fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
+# output:
+# fig="output/chr.contig/{chromosome}.contig.png",
+# outdir=directory("output/chr.contig/{chromosome}")
+# threads: 1
+# params:
+# app_path=config["app.path"]
+# shell:
+# """
+# mkdir {output.outdir}
+# base="{output.outdir}"
+# hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
- # Creating .bands file
- apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
- -s 5 \
- -f {input.fa} \
- > $base/{wildcards.chromosome}.gff
-
- #cat $base/{wildcards.chromosome}.gff
-
- awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
- sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
- > $base/{wildcards.chromosome}.bands
-
- #cat $base/{wildcards.chromosome}.bands
-
- # Creating bed like file
- cat {input.fai} | \
- cut -f1,2 | tr '\\t' ',' | \
- sed "s/,/,1,/" | \
- sed "1i chr\\tstart\\tend" | \
- tr ',' '\\t' \
- > $base/{wildcards.chromosome}.tsv
-
- #cat $base/{wildcards.chromosome}.tsv
-
- # Creating figure
- apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
- -b $base/{wildcards.chromosome}.bands \
- -t $base/{wildcards.chromosome}.tsv \
- -o {output.fig}
- """
-
-rule clustering:
- # Read ragtagged fastas and split chromosome sequences into according bins
- input:
- expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
- output:
- expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
- threads: workflow.cores
- params:
- app_path=config["app.path"],
- pan_name=config["name"]
- shell:
- """
- mkdir -p $(dirname {output[0]})
- apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
- --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
- for file in $(dirname {output[0]})/*.fa; do
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
- done
- """
-
-rule create_allAsm_syri_fig:
- # Create a SyRI figure containing all input assemblies
- input:
- ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
- qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
- output:
- fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
- wrkdir=directory('data/asm.syri/all')
- threads: 8
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir {output.wrkdir}
-
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {input.ref} \
- -q "{input.qry}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- """
-
-rule create_sglAsm_syri_fig:
- # Create a SyRI figure for a single input assembly
- input:
- ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
- qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
- output:
- fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
- wrkdir=directory('data/asm.syri/{haplotype}')
- threads: 4
- retries: 1
- resources:
- mem_gb=48
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir -p {output.wrkdir}
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {input.ref} \
- -q "{input.qry}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- """
-
-"""
+# # Creating .bands file
+# apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
+# -s 5 \
+# -f {input.fa} \
+# > $base/{wildcards.chromosome}.gff
+
+# #cat $base/{wildcards.chromosome}.gff
+
+# awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
+# sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
+# > $base/{wildcards.chromosome}.bands
+
+# #cat $base/{wildcards.chromosome}.bands
+
+# # Creating bed like file
+# cat {input.fai} | \
+# cut -f1,2 | tr '\\t' ',' | \
+# sed "s/,/,1,/" | \
+# sed "1i chr\\tstart\\tend" | \
+# tr ',' '\\t' \
+# > $base/{wildcards.chromosome}.tsv
+
+# #cat $base/{wildcards.chromosome}.tsv
+
+# # Creating figure
+# apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
+# -b $base/{wildcards.chromosome}.bands \
+# -t $base/{wildcards.chromosome}.tsv \
+# -o {output.fig}
+# """
+
+# rule clustering:
+# # Read ragtagged fastas and split chromosome sequences into according bins
+# input:
+# expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+# output:
+# expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
+# threads: workflow.cores
+# params:
+# app_path=config["app.path"],
+# pan_name=config["name"]
+# shell:
+# """
+# mkdir -p $(dirname {output[0]})
+# apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
+# --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
+# for file in $(dirname {output[0]})/*.fa; do
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
+# done
+# """
+
+# rule create_allAsm_syri_fig:
+# # Create a SyRI figure containing all input assemblies
+# input:
+# ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+# qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+# output:
+# fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
+# wrkdir=directory('data/asm.syri/all')
+# threads: 8
+# params:
+# app_path=config["app.path"]
+# shell:
+# """
+# mkdir {output.wrkdir}
+
+# bash scripts/getSyriFigs.sh \
+# -a {params.app_path} \
+# -t {threads} \
+# -d {output.wrkdir} \
+# -o $(basename {output.fig}) \
+# -r {input.ref} \
+# -q "{input.qry}"
+# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+# """
+
+# rule create_sglAsm_syri_fig:
+# # Create a SyRI figure for a single input assembly
+# input:
+# ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+# qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
+# output:
+# fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
+# wrkdir=directory('data/asm.syri/{haplotype}')
+# threads: 4
+# retries: 1
+# resources:
+# mem_gb=48
+# params:
+# app_path=config["app.path"]
+# shell:
+# """
+# mkdir -p {output.wrkdir}
+# bash scripts/getSyriFigs.sh \
+# -a {params.app_path} \
+# -t {threads} \
+# -d {output.wrkdir} \
+# -o $(basename {output.fig}) \
+# -r {input.ref} \
+# -q "{input.qry}"
+# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+# """
-Core section : Running PGGB
+# """
+# Core section : Running PGGB
+# """
-"""
+# rule create_pggb_input_syri_fig:
+# input:
+# fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
+# output:
+# fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
+# wrkdir=directory('data/chrInput/syri/{chromosome}')
+# threads: 8
+# params:
+# app_path=config["app.path"],
+# ref=config['reference']
+# shell:
+# """
+# mkdir {output.wrkdir}
+# refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
-rule create_pggb_input_syri_fig:
- input:
- fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
- output:
- fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
- wrkdir=directory('data/chrInput/syri/{chromosome}')
- threads: 8
- params:
- app_path=config["app.path"],
- ref=config['reference']
- shell:
- """
- mkdir {output.wrkdir}
- refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
-
- ## Creating single fasta from multifasta
- zcat {input.fasta} | awk -F"#" \
- '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
+# ## Creating single fasta from multifasta
+# zcat {input.fasta} | awk -F"#" \
+# '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
- ## Getting the list of sequences
- asmList=()
- for file in {output.wrkdir}/*.fa; do
- asm="$(basename $file .fa | cut -f1 -d"#").fa"
- mv $file "$(dirname $file)/$asm"
- asmList+=("$asm")
- done
-
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {output.wrkdir}/"${refname}.fa" \
- -q "${asmList[@]}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- rm {output.wrkdir}/*.fa
- """
-
-rule wfmash_on_chr:
- # Run wfmash on a specific chromosome input
- input:
- fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
- fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
- output:
- mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
- aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
- threads: 16
- params:
- app_path=config['app.path'],
- segment_length=config['wfmash.segment_length'],
- mapping_id=config['wfmash.mapping_id'],
- wfmash_sec=config['wfmash.secondary']
- log:
- cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
- time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
- cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
- time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
- shell:
- """
- ## Mapping
- /usr/bin/time -v -o {log.time_map} \
- apptainer exec {params.app_path}/pggb.sif wfmash \
- -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
- -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
- --tmp-base $(dirname {output.aln}) \
- {input.fa} --approx-map \
- 1> {output.mapping} \
- 2> >(tee {log.cmd_map} >&2)
-
- ## Aligning
- /usr/bin/time -v -o {log.time_aln} \
- apptainer exec {params.app_path}/pggb.sif wfmash \
- -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
- -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
- --tmp-base $(dirname {output.aln}) \
- {input.fa} -i {output.mapping} \
- --invert-filtering \
- 1> {output.aln} \
- 2> >(tee {log.cmd_aln} >&2)
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.mapping}
-
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.aln}
- """
-
-rule seqwish:
- # Run seqwish on alignement produced by wfmash
- input:
- fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
- aln=rules.wfmash_on_chr.output.aln
- output:
- temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
- threads: 8
- params:
- app_path=config['app.path'],
- seqwish=config['seqwish.params']
- log:
- cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
- time="logs/pggb/{chromosome}.seqwish.time.log"
- shell:
- """
- /usr/bin/time -v -o {log.time} \
- apptainer exec {params.app_path}/pggb.sif seqwish \
- -s {input.fa} -p {input.aln} -g {output} \
- {params.seqwish} -t {threads} \
- --temp-dir $(dirname {output}) -P 2>&1 | \
- tee {log.cmd}
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output}
- """
-
-rule gfaffix_on_chr:
- # Run gfaffix on seqwish graph
- input:
- rules.seqwish.output
- output:
- gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
- transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
- threads: 1
- params:
- app_path=config['app.path']
- log:
- time="logs/pggb/{chromosome}.gfaffix.time.log"
- shell:
- """
- /usr/bin/time -v -o {log.time} \
- apptainer exec {params.app_path}/pggb.sif gfaffix \
- {input} -o {output.gfa} -t {output.transform} \
- > /dev/null
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.gfa}
- """
-
-rule odgi_postprocessing:
- # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
- input:
- rules.gfaffix_on_chr.output.gfa
- output:
- gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- threads: 8
- params:
- app_path=config['app.path']
- log:
- cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
- time_build="logs/pggb/{chromosome}.odgi_build.time.log",
- cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
- time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
- cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
- time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
- cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
- time_view="logs/pggb/{chromosome}.odgi_view.time.log"
- shell:
- """
- OGfile="$(dirname {input})/$(basename {input} .gfa)"
-
- ## Converting to odgi format and optimizing namespace
- /usr/bin/time -v -o {log.time_build} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
- tee {log.cmd_build}
+# ## Getting the list of sequences
+# asmList=()
+# for file in {output.wrkdir}/*.fa; do
+# asm="$(basename $file .fa | cut -f1 -d"#").fa"
+# mv $file "$(dirname $file)/$asm"
+# asmList+=("$asm")
+# done
+
+# bash scripts/getSyriFigs.sh \
+# -a {params.app_path} \
+# -t {threads} \
+# -d {output.wrkdir} \
+# -o $(basename {output.fig}) \
+# -r {output.wrkdir}/"${refname}.fa" \
+# -q "${asmList[@]}"
+# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+# rm {output.wrkdir}/*.fa
+# """
+
+# rule wfmash_on_chr:
+# # Run wfmash on a specific chromosome input
+# input:
+# fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+# fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
+# output:
+# mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
+# aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
+# threads: 16
+# params:
+# app_path=config['app.path'],
+# segment_length=config['wfmash.segment_length'],
+# mapping_id=config['wfmash.mapping_id'],
+# wfmash_sec=config['wfmash.secondary']
+# log:
+# cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
+# time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
+# cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
+# time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
+# shell:
+# """
+# ## Mapping
+# /usr/bin/time -v -o {log.time_map} \
+# apptainer exec {params.app_path}/pggb.sif wfmash \
+# -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+# -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+# --tmp-base $(dirname {output.aln}) \
+# {input.fa} --approx-map \
+# 1> {output.mapping} \
+# 2> >(tee {log.cmd_map} >&2)
+
+# ## Aligning
+# /usr/bin/time -v -o {log.time_aln} \
+# apptainer exec {params.app_path}/pggb.sif wfmash \
+# -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+# -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+# --tmp-base $(dirname {output.aln}) \
+# {input.fa} -i {output.mapping} \
+# --invert-filtering \
+# 1> {output.aln} \
+# 2> >(tee {log.cmd_aln} >&2)
+
+# # Compressing
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} -k {output.mapping}
+
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} -k {output.aln}
+# """
+
+# rule seqwish:
+# # Run seqwish on alignement produced by wfmash
+# input:
+# fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+# aln=rules.wfmash_on_chr.output.aln
+# output:
+# temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
+# threads: 8
+# params:
+# app_path=config['app.path'],
+# seqwish=config['seqwish.params']
+# log:
+# cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
+# time="logs/pggb/{chromosome}.seqwish.time.log"
+# shell:
+# """
+# /usr/bin/time -v -o {log.time} \
+# apptainer exec {params.app_path}/pggb.sif seqwish \
+# -s {input.fa} -p {input.aln} -g {output} \
+# {params.seqwish} -t {threads} \
+# --temp-dir $(dirname {output}) -P 2>&1 | \
+# tee {log.cmd}
+
+# # Compressing
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} -k {output}
+# """
+
+# rule gfaffix_on_chr:
+# # Run gfaffix on seqwish graph
+# input:
+# rules.seqwish.output
+# output:
+# gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
+# transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
+# threads: 1
+# params:
+# app_path=config['app.path']
+# log:
+# time="logs/pggb/{chromosome}.gfaffix.time.log"
+# shell:
+# """
+# /usr/bin/time -v -o {log.time} \
+# apptainer exec {params.app_path}/pggb.sif gfaffix \
+# {input} -o {output.gfa} -t {output.transform} \
+# > /dev/null
+
+# # Compressing
+# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# -@ {threads} -k {output.gfa}
+# """
+
+# rule odgi_postprocessing:
+# # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
+# input:
+# rules.gfaffix_on_chr.output.gfa
+# output:
+# gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+# threads: 8
+# params:
+# app_path=config['app.path']
+# log:
+# cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
+# time_build="logs/pggb/{chromosome}.odgi_build.time.log",
+# cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
+# time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
+# cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
+# time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
+# cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
+# time_view="logs/pggb/{chromosome}.odgi_view.time.log"
+# shell:
+# """
+# OGfile="$(dirname {input})/$(basename {input} .gfa)"
+
+# ## Converting to odgi format and optimizing namespace
+# /usr/bin/time -v -o {log.time_build} \
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
+# tee {log.cmd_build}
- ## Unchoping the nodes (merges unitigs into single nodes)
- /usr/bin/time -v -o {log.time_unchop} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
- tee {log.cmd_unchop}
-
- ## Sorting the nodes
- /usr/bin/time -v -o {log.time_sort} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
- -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
- tee {log.cmd_sort}
-
- ## Exporting to gfa
- /usr/bin/time -v -o {log.time_view} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- view -i $OGfile.unchoped.sorted.og -g \
- 1> {output.gfa} \
- 2> >(tee {log.cmd_view} >&2)
-
- ## Removing .og files for space savings
- rm $(dirname {input})/*.og
-
- ## Adding metadata
- python scripts/getTags.py \
- --appdir {params.app_path} --config-file config.yaml \
- > "$(dirname {input})/metadata.txt"
- sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
-
- # Compressing
- # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- # -@ {threads} -k {output.gfa}
- """
-
-rule generate_graph_list:
- # Generate a text file containing all created graphs
- input:
- expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
- output:
- "data/chrGraphs/graphsList.txt"
- threads: 1
- run:
- with open(output[0], "w") as handle:
- for file in input:
- handle.write(file+"\n")
-
-rule graph_squeeze:
- # Using odgi to merge every subgraphs into a final one
- input:
- glist="data/chrGraphs/graphsList.txt",
- graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
- output:
- "output/pan1c."+config['name']+".gfa"
- threads: 16
- params:
- app_path=config['app.path']
- shell:
- """
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- view -t {threads} -P -i {output}.og -g > {output}
- rm {output}.og
- """
-
-rule graph_stats:
- # Using GFAstats to produce stats on every chromosome graphs
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
- pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
- threads: 4
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
- -g {input.graph} -P \
- -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
- -t {threads}
- """
-
-rule graph_figs:
- # Creating figures using odgi viz
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
- pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
- threads: 4
- params:
- app_path=config['app.path'],
- oneDviz=config['odgi.1Dviz.params'],
- pcov=config['odgi.pcov.params']
- shell:
- """
- ## 1D viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
-
- ## Pcov viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
- """
-
-rule aggregate_graphs_stats:
- # Reading and merging all stats files from chromosome graphs into a .tsv.
- input:
- genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
- output:
- genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
- --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
- --outputPaths {output.pathstats} --panname {params.pan_name}
- """
-
-rule final_graph_tagging:
- # Add metadata to the final GFA
- input:
- graph="output/pan1c."+config['name']+".gfa",
- output:
- "output/pan1c."+config['name']+".gfa.metadata"
- threads: 1
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- python scripts/getTags.py \
- --appdir {params.app_path} --config-file config.yaml > {output}
- sed -i '/^H/r {output}' {input.graph}
- """
-
-rule pggb_input_stats:
- # Produces statistics on pggb input sequences
- input:
- flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
- output:
- "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
- -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
- """
-
-rule core_statistics:
- # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
- input:
- chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
- chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
- output:
- tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
- dir=directory("output/pggb.usage.figs")
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- mkdir -p {output.dir}
- apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
- --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
- --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
- """
+# ## Unchoping the nodes (merges unitigs into single nodes)
+# /usr/bin/time -v -o {log.time_unchop} \
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
+# tee {log.cmd_unchop}
+
+# ## Sorting the nodes
+# /usr/bin/time -v -o {log.time_sort} \
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
+# -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
+# tee {log.cmd_sort}
+
+# ## Exporting to gfa
+# /usr/bin/time -v -o {log.time_view} \
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# view -i $OGfile.unchoped.sorted.og -g \
+# 1> {output.gfa} \
+# 2> >(tee {log.cmd_view} >&2)
+
+# ## Removing .og files for space savings
+# rm $(dirname {input})/*.og
+
+# ## Adding metadata
+# python scripts/getTags.py \
+# --appdir {params.app_path} --config-file config.yaml \
+# > "$(dirname {input})/metadata.txt"
+# sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
+
+# # Compressing
+# # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+# # -@ {threads} -k {output.gfa}
+# """
+
+# rule generate_graph_list:
+# # Generate a text file containing all created graphs
+# input:
+# expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+# output:
+# "data/chrGraphs/graphsList.txt"
+# threads: 1
+# run:
+# with open(output[0], "w") as handle:
+# for file in input:
+# handle.write(file+"\n")
-"""
+# rule graph_squeeze:
+# # Using odgi to merge every subgraphs into a final one
+# input:
+# glist="data/chrGraphs/graphsList.txt",
+# graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+# output:
+# "output/pan1c."+config['name']+".gfa"
+# threads: 16
+# params:
+# app_path=config['app.path']
+# shell:
+# """
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# view -t {threads} -P -i {output}.og -g > {output}
+# rm {output}.og
+# """
+
+# rule graph_stats:
+# # Using GFAstats to produce stats on every chromosome graphs
+# input:
+# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+# output:
+# genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
+# pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
+# threads: 4
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name']
+# shell:
+# """
+# apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
+# -g {input.graph} -P \
+# -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
+# -t {threads}
+# """
+
+# rule graph_figs:
+# # Creating figures using odgi viz
+# input:
+# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+# output:
+# oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
+# pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
+# threads: 4
+# params:
+# app_path=config['app.path'],
+# oneDviz=config['odgi.1Dviz.params'],
+# pcov=config['odgi.pcov.params']
+# shell:
+# """
+# ## 1D viz
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
+
+# ## Pcov viz
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
+# """
+
+# rule aggregate_graphs_stats:
+# # Reading and merging all stats files from chromosome graphs into a .tsv.
+# input:
+# genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
+# output:
+# genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+# pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name']
+# shell:
+# """
+# apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
+# --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
+# --outputPaths {output.pathstats} --panname {params.pan_name}
+# """
+
+# rule final_graph_tagging:
+# # Add metadata to the final GFA
+# input:
+# graph="output/pan1c."+config['name']+".gfa",
+# output:
+# "output/pan1c."+config['name']+".gfa.metadata"
+# threads: 1
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name']
+# shell:
+# """
+# python scripts/getTags.py \
+# --appdir {params.app_path} --config-file config.yaml > {output}
+# sed -i '/^H/r {output}' {input.graph}
+# """
+
+# rule pggb_input_stats:
+# # Produces statistics on pggb input sequences
+# input:
+# flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+# output:
+# "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name']
+# shell:
+# """
+# apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
+# -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
+# """
-Post-processing section :
- The graph for each chromosome are made as well as some basic statistics.
- In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
- It also contains rules to use the graph itself.
+# rule core_statistics:
+# # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
+# input:
+# chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
+# chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+# output:
+# tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
+# dir=directory("output/pggb.usage.figs")
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name']
+# shell:
+# """
+# mkdir -p {output.dir}
+# apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
+# --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
+# --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
+# """
-"""
-rule get_pav:
- # Create PAV matrix readable by panache for a given chromosome scale graph
- input:
- "data/chrGraphs/graphsList.txt"
- output:
- directory("output/pav.matrices")
- threads: 16
- params:
- app_path=config['app.path']
- run:
- shell("mkdir {output}")
- # Getting the list of graphs
- with open(input[0]) as handle:
- graphList = [graph.rstrip("\n") for graph in handle.readlines()]
- # Iterating over graphs
- for graph in graphList:
- shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
-
-rule panacus_stats:
- # Produces panacus reports for a chromosome graph
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
- params:
- app_path=config['app.path'],
- pan_name=config['name'],
- refname=config['reference']
- threads: 8
- shell:
- """
- bash scripts/getPanacusHG.sh \
- -g {input.graph} \
- -r $(basename {params.refname} .fa.gz) \
- -d data/chrGraphs/{wildcards.chromosome} \
- -o {output.html} \
- -a {params.app_path} \
- -t {threads}
- """
-
-rule create_pan1c_report_fig:
- # Produces a markdown report figure of chromosomes graphs
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
- contigfig="output/chr.contig/{chromosome}.contig.png",
- output:
- odgifig=temp("tmp/{chromosome}.odgi.png"),
- namefig=temp("tmp/{chromosome}.name.png"),
- reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
- threads: 4
- params:
- app_path=config['app.path']
- shell:
- """
- ## Odgi 1D viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
-
- ## Getting legend from contig figure
- convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
-
- odgheight=$(identify -ping -format '%h' {output.odgifig})
- ctgheight=$(identify -ping -format '%h' {input.contigfig})
-
- combinedheight=$(($odgheight+$ctgheight))
-
- echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
-
- ## Creating empty canvas ad adding other figures to it
- convert -size "3300x$combinedheight" xc:white {output.reportfig}
- composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
- composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
- composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
- """
-
-rule create_pan1c_report:
- # Produces a markdown report of chromosomes graphs
- input:
- figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
- genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
- output:
- reportfig="output/pan1c."+config['name']+".report.md"
- threads: 4
- params:
- app_path=config['app.path']
- run:
- shell("touch {output.reportfig}")
-
- # Adding Summary
- ## To Do
-
- # Adding General stats
- shell("echo '# General stats' >> {output.reportfig}")
- shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
-
- # Adding Path stats
- shell("echo '# Path stats' >> {output.reportfig}")
- shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
-
- # Adding chromosomes figures
- fig_list = [fig for fig in input.figs]
- print(fig_list)
- fig_list.sort()
+# """
+# Post-processing section :
+# The graph for each chromosome are made as well as some basic statistics.
+# In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
+# It also contains rules to use the graph itself.
+# """
+# rule get_pav:
+# # Create PAV matrix readable by panache for a given chromosome scale graph
+# input:
+# "data/chrGraphs/graphsList.txt"
+# output:
+# directory("output/pav.matrices")
+# threads: 16
+# params:
+# app_path=config['app.path']
+# run:
+# shell("mkdir {output}")
+# # Getting the list of graphs
+# with open(input[0]) as handle:
+# graphList = [graph.rstrip("\n") for graph in handle.readlines()]
+# # Iterating over graphs
+# for graph in graphList:
+# shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
+
+# rule panacus_stats:
+# # Produces panacus reports for a chromosome graph
+# input:
+# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+# output:
+# html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
+# params:
+# app_path=config['app.path'],
+# pan_name=config['name'],
+# refname=config['reference']
+# threads: 8
+# shell:
+# """
+# bash scripts/getPanacusHG.sh \
+# -g {input.graph} \
+# -r $(basename {params.refname} .fa.gz) \
+# -d data/chrGraphs/{wildcards.chromosome} \
+# -o {output.html} \
+# -a {params.app_path} \
+# -t {threads}
+# """
+
+# rule create_pan1c_report_fig:
+# # Produces a markdown report figure of chromosomes graphs
+# input:
+# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
+# contigfig="output/chr.contig/{chromosome}.contig.png",
+# output:
+# odgifig=temp("tmp/{chromosome}.odgi.png"),
+# namefig=temp("tmp/{chromosome}.name.png"),
+# reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
+# threads: 4
+# params:
+# app_path=config['app.path']
+# shell:
+# """
+# ## Odgi 1D viz
+# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+# viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
+
+# ## Getting legend from contig figure
+# convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
+
+# odgheight=$(identify -ping -format '%h' {output.odgifig})
+# ctgheight=$(identify -ping -format '%h' {input.contigfig})
+
+# combinedheight=$(($odgheight+$ctgheight))
+
+# echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
+
+# ## Creating empty canvas ad adding other figures to it
+# convert -size "3300x$combinedheight" xc:white {output.reportfig}
+# composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
+# composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
+# composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
+# """
+
+# rule create_pan1c_report:
+# # Produces a markdown report of chromosomes graphs
+# input:
+# figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
+# genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+# pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+# output:
+# reportfig="output/pan1c."+config['name']+".report.md"
+# threads: 4
+# params:
+# app_path=config['app.path']
+# run:
+# shell("touch {output.reportfig}")
+
+# # Adding Summary
+# ## To Do
+
+# # Adding General stats
+# shell("echo '# General stats' >> {output.reportfig}")
+# shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
+# shell("echo '' >> {output.reportfig}")
+
+# # Adding Path stats
+# shell("echo '# Path stats' >> {output.reportfig}")
+# shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
+# shell("echo '' >> {output.reportfig}")
+
+# # Adding chromosomes figures
+# fig_list = [fig for fig in input.figs]
+# print(fig_list)
+# fig_list.sort()
- shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
- for fig in fig_list:
- basename=os.path.basename(fig)
- chr_name=basename.split('.')[1]
+# shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
+# for fig in fig_list:
+# basename=os.path.basename(fig)
+# chr_name=basename.split('.')[1]
- shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
\ No newline at end of file
+# shell("echo '## {chr_name}' >> {output.reportfig}")
+# shell("echo '' >> {output.reportfig}")
+# shell("echo '' >> {output.reportfig}")
\ No newline at end of file
diff --git a/rules/core.smk b/rules/core.smk
new file mode 100644
index 0000000..5473943
--- /dev/null
+++ b/rules/core.smk
@@ -0,0 +1,346 @@
+"""
+Core section : Running PGGB on each chromosome and generating whole pangenome -------------------
+"""
+
+rule create_pggb_input_syri_fig:
+ input:
+ fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
+ output:
+ fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
+ wrkdir=directory('data/chrInput/syri/{chromosome}')
+ threads: 8
+ params:
+ app_path=config["app.path"],
+ ref=config['reference']
+ shell:
+ """
+ mkdir {output.wrkdir}
+ refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
+
+ ## Creating single fasta from multifasta
+ zcat {input.fasta} | awk -F"#" \
+ '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
+
+ ## Getting the list of sequences
+ asmList=()
+ for file in {output.wrkdir}/*.fa; do
+ asm="$(basename $file .fa | cut -f1 -d"#").fa"
+ mv $file "$(dirname $file)/$asm"
+ asmList+=("$asm")
+ done
+
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {output.wrkdir}/"${refname}.fa" \
+ -q "${asmList[@]}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ rm {output.wrkdir}/*.fa
+ """
+
+rule wfmash_on_chr:
+ # Run wfmash on a specific chromosome input
+ input:
+ fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+ fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
+ output:
+ mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
+ aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
+ threads: 16
+ params:
+ app_path=config['app.path'],
+ segment_length=config['wfmash.segment_length'],
+ mapping_id=config['wfmash.mapping_id'],
+ wfmash_sec=config['wfmash.secondary']
+ log:
+ cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
+ time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
+ cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
+ time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
+ shell:
+ """
+ ## Mapping
+ /usr/bin/time -v -o {log.time_map} \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} --approx-map \
+ 1> {output.mapping} \
+ 2> >(tee {log.cmd_map} >&2)
+
+ ## Aligning
+ /usr/bin/time -v -o {log.time_aln} \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} -i {output.mapping} \
+ --invert-filtering \
+ 1> {output.aln} \
+ 2> >(tee {log.cmd_aln} >&2)
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.mapping}
+
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.aln}
+ """
+
+rule seqwish:
+ # Run seqwish on alignement produced by wfmash
+ input:
+ fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+ aln=rules.wfmash_on_chr.output.aln
+ output:
+ temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
+ threads: 8
+ params:
+ app_path=config['app.path'],
+ seqwish=config['seqwish.params']
+ log:
+ cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
+ time="logs/pggb/{chromosome}.seqwish.time.log"
+ shell:
+ """
+ /usr/bin/time -v -o {log.time} \
+ apptainer exec {params.app_path}/pggb.sif seqwish \
+ -s {input.fa} -p {input.aln} -g {output} \
+ {params.seqwish} -t {threads} \
+ --temp-dir $(dirname {output}) -P 2>&1 | \
+ tee {log.cmd}
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output}
+ """
+
+rule gfaffix_on_chr:
+ # Run gfaffix on seqwish graph
+ input:
+ rules.seqwish.output
+ output:
+ gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
+ transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
+ threads: 1
+ params:
+ app_path=config['app.path']
+ log:
+ time="logs/pggb/{chromosome}.gfaffix.time.log"
+ shell:
+ """
+ /usr/bin/time -v -o {log.time} \
+ apptainer exec {params.app_path}/pggb.sif gfaffix \
+ {input} -o {output.gfa} -t {output.transform} \
+ > /dev/null
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.gfa}
+ """
+
+rule odgi_postprocessing:
+ # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
+ input:
+ rules.gfaffix_on_chr.output.gfa
+ output:
+ gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ threads: 8
+ params:
+ app_path=config['app.path']
+ log:
+ cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
+ time_build="logs/pggb/{chromosome}.odgi_build.time.log",
+ cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
+ time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
+ cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
+ time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
+ cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
+ time_view="logs/pggb/{chromosome}.odgi_view.time.log"
+ shell:
+ """
+ OGfile="$(dirname {input})/$(basename {input} .gfa)"
+
+ ## Converting to odgi format and optimizing namespace
+ /usr/bin/time -v -o {log.time_build} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
+ tee {log.cmd_build}
+
+ ## Unchoping the nodes (merges unitigs into single nodes)
+ /usr/bin/time -v -o {log.time_unchop} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
+ tee {log.cmd_unchop}
+
+ ## Sorting the nodes
+ /usr/bin/time -v -o {log.time_sort} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
+ -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
+ tee {log.cmd_sort}
+
+ ## Exporting to gfa
+ /usr/bin/time -v -o {log.time_view} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ view -i $OGfile.unchoped.sorted.og -g \
+ 1> {output.gfa} \
+ 2> >(tee {log.cmd_view} >&2)
+
+ ## Removing .og files for space savings
+ rm $(dirname {input})/*.og
+
+ ## Adding metadata
+ python scripts/getTags.py \
+ --appdir {params.app_path} --config-file config.yaml \
+ > "$(dirname {input})/metadata.txt"
+ sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
+
+ # Compressing
+ # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ # -@ {threads} -k {output.gfa}
+ """
+
+rule generate_graph_list:
+ # Generate a text file containing all created graphs
+ input:
+ expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+ output:
+ "data/chrGraphs/graphsList.txt"
+ threads: 1
+ run:
+ with open(output[0], "w") as handle:
+ for file in input:
+ handle.write(file+"\n")
+
+rule graph_squeeze:
+ # Using odgi to merge every subgraphs into a final one
+ input:
+ glist="data/chrGraphs/graphsList.txt",
+ graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+ output:
+ "output/pan1c."+config['name']+".gfa"
+ threads: 16
+ params:
+ app_path=config['app.path']
+ shell:
+ """
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ view -t {threads} -P -i {output}.og -g > {output}
+ rm {output}.og
+ """
+
+rule graph_stats:
+ # Using GFAstats to produce stats on every chromosome graphs
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
+ pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
+ threads: 4
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
+ -g {input.graph} -P \
+ -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
+ -t {threads}
+ """
+
+rule graph_figs:
+ # Creating figures using odgi viz
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
+ pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
+ threads: 4
+ params:
+ app_path=config['app.path'],
+ oneDviz=config['odgi.1Dviz.params'],
+ pcov=config['odgi.pcov.params']
+ shell:
+ """
+ ## 1D viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
+
+ ## Pcov viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
+ """
+
+rule aggregate_graphs_stats:
+ # Reading and merging all stats files from chromosome graphs into a .tsv.
+ input:
+ genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
+ output:
+ genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
+ --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
+ --outputPaths {output.pathstats} --panname {params.pan_name}
+ """
+
+rule final_graph_tagging:
+ # Add metadata to the final GFA
+ input:
+ graph="output/pan1c."+config['name']+".gfa",
+ output:
+ "output/pan1c."+config['name']+".gfa.metadata"
+ threads: 1
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ python scripts/getTags.py \
+ --appdir {params.app_path} --config-file config.yaml > {output}
+ sed -i '/^H/r {output}' {input.graph}
+ """
+
+rule pggb_input_stats:
+ # Produces statistics on pggb input sequences
+ input:
+ flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ output:
+ "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
+ -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
+ """
+
+rule core_statistics:
+ # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
+ input:
+ chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
+ chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ output:
+ tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
+ dir=directory("output/pggb.usage.figs")
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ mkdir -p {output.dir}
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
+ --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
+ --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
+ """
\ No newline at end of file
diff --git a/rules/post-analysis.smk b/rules/post-analysis.smk
new file mode 100644
index 0000000..3041501
--- /dev/null
+++ b/rules/post-analysis.smk
@@ -0,0 +1,118 @@
+"""
+Post-analysis section ---------------------------------------------------------------------------
+"""
+rule get_pav:
+ # Create PAV matrix readable by panache for a given chromosome scale graph
+ input:
+ "data/chrGraphs/graphsList.txt"
+ output:
+ directory("output/pav.matrices")
+ threads: 16
+ params:
+ app_path=config['app.path']
+ run:
+ shell("mkdir {output}")
+ # Getting the list of graphs
+ with open(input[0]) as handle:
+ graphList = [graph.rstrip("\n") for graph in handle.readlines()]
+ # Iterating over graphs
+ for graph in graphList:
+ shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
+
+rule panacus_stats:
+ # Produces panacus reports for a chromosome graph
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name'],
+ refname=config['reference']
+ threads: 8
+ shell:
+ """
+ bash scripts/getPanacusHG.sh \
+ -g {input.graph} \
+ -r $(basename {params.refname} .fa.gz) \
+ -d data/chrGraphs/{wildcards.chromosome} \
+ -o {output.html} \
+ -a {params.app_path} \
+ -t {threads}
+ """
+
+rule create_pan1c_report_fig:
+ # Produces a markdown report figure of chromosomes graphs
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
+ contigfig="output/chr.contig/{chromosome}.contig.png",
+ output:
+ odgifig=temp("tmp/{chromosome}.odgi.png"),
+ namefig=temp("tmp/{chromosome}.name.png"),
+ reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
+ threads: 4
+ params:
+ app_path=config['app.path']
+ shell:
+ """
+ ## Odgi 1D viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
+
+ ## Getting legend from contig figure
+ convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
+
+ odgheight=$(identify -ping -format '%h' {output.odgifig})
+ ctgheight=$(identify -ping -format '%h' {input.contigfig})
+
+ combinedheight=$(($odgheight+$ctgheight))
+
+ echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
+
+ ## Creating empty canvas ad adding other figures to it
+ convert -size "3300x$combinedheight" xc:white {output.reportfig}
+ composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
+ composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
+ composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
+ """
+
+rule create_pan1c_report:
+ # Produces a markdown report of chromosomes graphs
+ input:
+ figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
+ genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ output:
+ reportfig="output/pan1c."+config['name']+".report.md"
+ threads: 4
+ params:
+ app_path=config['app.path']
+ run:
+ shell("touch {output.reportfig}")
+
+ # Adding Summary
+ ## To Do
+
+ # Adding General stats
+ shell("echo '# General stats' >> {output.reportfig}")
+ shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding Path stats
+ shell("echo '# Path stats' >> {output.reportfig}")
+ shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding chromosomes figures
+ fig_list = [fig for fig in input.figs]
+ print(fig_list)
+ fig_list.sort()
+
+ shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
+ for fig in fig_list:
+ basename=os.path.basename(fig)
+ chr_name=basename.split('.')[1]
+
+ shell("echo '## {chr_name}' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
\ No newline at end of file
diff --git a/rules/pre-processing.smk b/rules/pre-processing.smk
new file mode 100644
index 0000000..3580108
--- /dev/null
+++ b/rules/pre-processing.smk
@@ -0,0 +1,185 @@
+"""
+Pre-processing section : preparing haplotypes ----------------------------------------------------
+"""
+rule ragtag_scaffolding:
+ # Scaffold input haplotype against the reference to infer chromosome scale sequences
+ input:
+ ref="data/haplotypes/"+config['reference'],
+ reffai="data/haplotypes/"+config['reference']+".fai",
+ refgzi="data/haplotypes/"+config['reference']+".gzi",
+ fa="data/haplotypes/{haplotype}.fa.gz"
+ output:
+ fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
+ tar="data/hap.ragtagged/{haplotype}.tar.gz"
+ threads: 8
+ retries: 1
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ bash scripts/ragtagChromInfer.sh \
+ -d $(dirname {output.fa})/{wildcards.haplotype} \
+ -a {params.app_path} \
+ -t {threads} \
+ -r {input.ref} \
+ -q {input.fa} \
+ -o {output.fa}
+
+ #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
+ # echo "Error : Empty final fasta"
+ # exit 1
+ #fi
+ """
+
+rule quast_stats:
+ # Run Quast on ragtagged genomes
+ input:
+ fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
+ ref="data/haplotypes/"+config['reference']
+ output:
+ report="output/quast/"+config['name']+".quast.report.html"
+ threads: 8
+ params:
+ app_path=config["app.path"],
+ pan_name=config["name"]
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif quast.py \
+ -t {threads} \
+ -o "$(dirname {output.report})" \
+ -r {input.ref} \
+ --plots-format png \
+ --no-read-stats \
+ --no-icarus \
+ -s \
+ --large \
+ {input.fas}
+
+ # Compressing temporary files
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
+
+ mv $(dirname {output.report})/report.html {output.report}
+ """
+
+rule contig_position:
+ # Produce figures with contig positions
+ input:
+ fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
+ fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
+ output:
+ fig="output/chr.contig/{chromosome}.contig.png",
+ outdir=directory("output/chr.contig/{chromosome}")
+ threads: 1
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir {output.outdir}
+ base="{output.outdir}"
+ hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
+
+ # Creating .bands file
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
+ -s 5 \
+ -f {input.fa} \
+ > $base/{wildcards.chromosome}.gff
+
+ #cat $base/{wildcards.chromosome}.gff
+
+ awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
+ sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
+ > $base/{wildcards.chromosome}.bands
+
+ #cat $base/{wildcards.chromosome}.bands
+
+ # Creating bed like file
+ cat {input.fai} | \
+ cut -f1,2 | tr '\\t' ',' | \
+ sed "s/,/,1,/" | \
+ sed "1i chr\\tstart\\tend" | \
+ tr ',' '\\t' \
+ > $base/{wildcards.chromosome}.tsv
+
+ #cat $base/{wildcards.chromosome}.tsv
+
+ # Creating figure
+ apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
+ -b $base/{wildcards.chromosome}.bands \
+ -t $base/{wildcards.chromosome}.tsv \
+ -o {output.fig}
+ """
+
+rule clustering:
+ # Read ragtagged fastas and split chromosome sequences into according bins
+ input:
+ expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+ output:
+ expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
+ threads: workflow.cores
+ params:
+ app_path=config["app.path"],
+ pan_name=config["name"]
+ shell:
+ """
+ mkdir -p $(dirname {output[0]})
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
+ --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
+ for file in $(dirname {output[0]})/*.fa; do
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
+ done
+ """
+
+rule create_allAsm_syri_fig:
+ # Create a SyRI figure containing all input assemblies
+ input:
+ ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+ qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+ output:
+ fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
+ wrkdir=directory('data/asm.syri/all')
+ threads: 8
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir {output.wrkdir}
+
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {input.ref} \
+ -q "{input.qry}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ """
+
+rule create_sglAsm_syri_fig:
+ # Create a SyRI figure for a single input assembly
+ input:
+ ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+ qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
+ output:
+ fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
+ wrkdir=directory('data/asm.syri/{haplotype}')
+ threads: 4
+ retries: 1
+ resources:
+ mem_gb=48
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir -p {output.wrkdir}
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {input.ref} \
+ -q "{input.qry}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ """
\ No newline at end of file
--
GitLab
From b6252858bb0f5c45e42b29ed5021f27283520905 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:50:59 +0200
Subject: [PATCH 35/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 0577e00..26409c2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -54,7 +54,7 @@ def which_analysis():
if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures
analysis_inputs.append(
- expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF),
+ expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES),
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
--
GitLab
From 49764da51cf0554ed70f701e0b3419f76c6742c8 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:53:14 +0200
Subject: [PATCH 36/86] Update Snakefile
---
Snakefile | 372 +++++++++++++++++++++++++++---------------------------
1 file changed, 186 insertions(+), 186 deletions(-)
diff --git a/Snakefile b/Snakefile
index 26409c2..2f20878 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,7 +1,7 @@
configfile: "config.yaml"
include: "rules/tools.smk"
-include: "rules/pre-processing.smk"
+#include: "rules/pre-processing.smk"
include: "rules/core.smk"
include: "rules/post-analysis.smk"
@@ -54,7 +54,7 @@ def which_analysis():
if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures
analysis_inputs.append(
- expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES),
+ expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF),
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
@@ -99,191 +99,191 @@ rule all:
# "apptainer run --app samtools {params.app_path}/PanGeTools.sif "
# "faidx {input.fa}"
-# """
-# Pre-processing section : preparing pggb inputs ---------------------------------------------------
-# """
-# rule ragtag_scaffolding:
-# # Scaffold input haplotype against the reference to infer chromosome scale sequences
-# input:
-# ref="data/haplotypes/"+config['reference'],
-# reffai="data/haplotypes/"+config['reference']+".fai",
-# refgzi="data/haplotypes/"+config['reference']+".gzi",
-# fa="data/haplotypes/{haplotype}.fa.gz"
-# output:
-# fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
-# tar="data/hap.ragtagged/{haplotype}.tar.gz"
-# threads: 8
-# retries: 1
-# params:
-# app_path=config["app.path"]
-# shell:
-# """
-# bash scripts/ragtagChromInfer.sh \
-# -d $(dirname {output.fa})/{wildcards.haplotype} \
-# -a {params.app_path} \
-# -t {threads} \
-# -r {input.ref} \
-# -q {input.fa} \
-# -o {output.fa}
-
-# #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
-# # echo "Error : Empty final fasta"
-# # exit 1
-# #fi
-# """
-
-# rule quast_stats:
-# # Run Quast on ragtagged genomes
-# input:
-# fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
-# ref="data/haplotypes/"+config['reference']
-# output:
-# report="output/quast/"+config['name']+".quast.report.html"
-# threads: 8
-# params:
-# app_path=config["app.path"],
-# pan_name=config["name"]
-# shell:
-# """
-# apptainer run {params.app_path}/pan1c-env.sif quast.py \
-# -t {threads} \
-# -o "$(dirname {output.report})" \
-# -r {input.ref} \
-# --plots-format png \
-# --no-read-stats \
-# --no-icarus \
-# -s \
-# --large \
-# {input.fas}
-
-# # Compressing temporary files
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
-
-# mv $(dirname {output.report})/report.html {output.report}
-# """
-
-# rule contig_position:
-# # Produce figures with contig positions
-# input:
-# fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
-# fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
-# output:
-# fig="output/chr.contig/{chromosome}.contig.png",
-# outdir=directory("output/chr.contig/{chromosome}")
-# threads: 1
-# params:
-# app_path=config["app.path"]
-# shell:
-# """
-# mkdir {output.outdir}
-# base="{output.outdir}"
-# hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
+"""
+Pre-processing section : preparing pggb inputs ---------------------------------------------------
+"""
+rule ragtag_scaffolding:
+ # Scaffold input haplotype against the reference to infer chromosome scale sequences
+ input:
+ ref="data/haplotypes/"+config['reference'],
+ reffai="data/haplotypes/"+config['reference']+".fai",
+ refgzi="data/haplotypes/"+config['reference']+".gzi",
+ fa="data/haplotypes/{haplotype}.fa.gz"
+ output:
+ fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
+ tar="data/hap.ragtagged/{haplotype}.tar.gz"
+ threads: 8
+ retries: 1
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ bash scripts/ragtagChromInfer.sh \
+ -d $(dirname {output.fa})/{wildcards.haplotype} \
+ -a {params.app_path} \
+ -t {threads} \
+ -r {input.ref} \
+ -q {input.fa} \
+ -o {output.fa}
+
+ #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
+ # echo "Error : Empty final fasta"
+ # exit 1
+ #fi
+ """
+
+rule quast_stats:
+ # Run Quast on ragtagged genomes
+ input:
+ fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
+ ref="data/haplotypes/"+config['reference']
+ output:
+ report="output/quast/"+config['name']+".quast.report.html"
+ threads: 8
+ params:
+ app_path=config["app.path"],
+ pan_name=config["name"]
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif quast.py \
+ -t {threads} \
+ -o "$(dirname {output.report})" \
+ -r {input.ref} \
+ --plots-format png \
+ --no-read-stats \
+ --no-icarus \
+ -s \
+ --large \
+ {input.fas}
+
+ # Compressing temporary files
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
+
+ mv $(dirname {output.report})/report.html {output.report}
+ """
+
+rule contig_position:
+ # Produce figures with contig positions
+ input:
+ fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
+ fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
+ output:
+ fig="output/chr.contig/{chromosome}.contig.png",
+ outdir=directory("output/chr.contig/{chromosome}")
+ threads: 1
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir {output.outdir}
+ base="{output.outdir}"
+ hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
-# # Creating .bands file
-# apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
-# -s 5 \
-# -f {input.fa} \
-# > $base/{wildcards.chromosome}.gff
-
-# #cat $base/{wildcards.chromosome}.gff
-
-# awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
-# sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
-# > $base/{wildcards.chromosome}.bands
-
-# #cat $base/{wildcards.chromosome}.bands
-
-# # Creating bed like file
-# cat {input.fai} | \
-# cut -f1,2 | tr '\\t' ',' | \
-# sed "s/,/,1,/" | \
-# sed "1i chr\\tstart\\tend" | \
-# tr ',' '\\t' \
-# > $base/{wildcards.chromosome}.tsv
-
-# #cat $base/{wildcards.chromosome}.tsv
-
-# # Creating figure
-# apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
-# -b $base/{wildcards.chromosome}.bands \
-# -t $base/{wildcards.chromosome}.tsv \
-# -o {output.fig}
-# """
-
-# rule clustering:
-# # Read ragtagged fastas and split chromosome sequences into according bins
-# input:
-# expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
-# output:
-# expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
-# threads: workflow.cores
-# params:
-# app_path=config["app.path"],
-# pan_name=config["name"]
-# shell:
-# """
-# mkdir -p $(dirname {output[0]})
-# apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
-# --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
-# for file in $(dirname {output[0]})/*.fa; do
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
-# done
-# """
-
-# rule create_allAsm_syri_fig:
-# # Create a SyRI figure containing all input assemblies
-# input:
-# ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
-# qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
-# output:
-# fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
-# wrkdir=directory('data/asm.syri/all')
-# threads: 8
-# params:
-# app_path=config["app.path"]
-# shell:
-# """
-# mkdir {output.wrkdir}
-
-# bash scripts/getSyriFigs.sh \
-# -a {params.app_path} \
-# -t {threads} \
-# -d {output.wrkdir} \
-# -o $(basename {output.fig}) \
-# -r {input.ref} \
-# -q "{input.qry}"
-# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
-# """
-
-# rule create_sglAsm_syri_fig:
-# # Create a SyRI figure for a single input assembly
-# input:
-# ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
-# qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
-# output:
-# fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
-# wrkdir=directory('data/asm.syri/{haplotype}')
-# threads: 4
-# retries: 1
-# resources:
-# mem_gb=48
-# params:
-# app_path=config["app.path"]
-# shell:
-# """
-# mkdir -p {output.wrkdir}
-# bash scripts/getSyriFigs.sh \
-# -a {params.app_path} \
-# -t {threads} \
-# -d {output.wrkdir} \
-# -o $(basename {output.fig}) \
-# -r {input.ref} \
-# -q "{input.qry}"
-# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
-# """
+ # Creating .bands file
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
+ -s 5 \
+ -f {input.fa} \
+ > $base/{wildcards.chromosome}.gff
+
+ #cat $base/{wildcards.chromosome}.gff
+
+ awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
+ sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
+ > $base/{wildcards.chromosome}.bands
+
+ #cat $base/{wildcards.chromosome}.bands
+
+ # Creating bed like file
+ cat {input.fai} | \
+ cut -f1,2 | tr '\\t' ',' | \
+ sed "s/,/,1,/" | \
+ sed "1i chr\\tstart\\tend" | \
+ tr ',' '\\t' \
+ > $base/{wildcards.chromosome}.tsv
+
+ #cat $base/{wildcards.chromosome}.tsv
+
+ # Creating figure
+ apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
+ -b $base/{wildcards.chromosome}.bands \
+ -t $base/{wildcards.chromosome}.tsv \
+ -o {output.fig}
+ """
+
+rule clustering:
+ # Read ragtagged fastas and split chromosome sequences into according bins
+ input:
+ expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+ output:
+ expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
+ threads: workflow.cores
+ params:
+ app_path=config["app.path"],
+ pan_name=config["name"]
+ shell:
+ """
+ mkdir -p $(dirname {output[0]})
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
+ --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
+ for file in $(dirname {output[0]})/*.fa; do
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
+ done
+ """
+
+rule create_allAsm_syri_fig:
+ # Create a SyRI figure containing all input assemblies
+ input:
+ ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+ qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
+ output:
+ fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
+ wrkdir=directory('data/asm.syri/all')
+ threads: 8
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir {output.wrkdir}
+
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {input.ref} \
+ -q "{input.qry}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ """
+
+rule create_sglAsm_syri_fig:
+ # Create a SyRI figure for a single input assembly
+ input:
+ ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
+ qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
+ output:
+ fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
+ wrkdir=directory('data/asm.syri/{haplotype}')
+ threads: 4
+ retries: 1
+ resources:
+ mem_gb=48
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ mkdir -p {output.wrkdir}
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {input.ref} \
+ -q "{input.qry}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ """
# """
# Core section : Running PGGB
--
GitLab
From 97b12904ca91a4400f58768558b83fc92a6f50e8 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 16:59:15 +0200
Subject: [PATCH 37/86] Revert "Update Snakefile"
This reverts commit 8b78a0262b616a724a1b13074dcab1ac45515c0d.
---
Snakefile | 953 +++++++++++++++++++--------------------
rules/core.smk | 346 --------------
rules/post-analysis.smk | 118 -----
rules/pre-processing.smk | 185 --------
4 files changed, 469 insertions(+), 1133 deletions(-)
delete mode 100644 rules/core.smk
delete mode 100644 rules/post-analysis.smk
delete mode 100644 rules/pre-processing.smk
diff --git a/Snakefile b/Snakefile
index 2f20878..e3818f2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -1,9 +1,7 @@
configfile: "config.yaml"
include: "rules/tools.smk"
-#include: "rules/pre-processing.smk"
-include: "rules/core.smk"
-include: "rules/post-analysis.smk"
+
## Modules
import os
@@ -82,23 +80,6 @@ rule all:
"output/pan1c."+config['name']+".gfa.metadata", # Metadata for the final (also in top of gfa files as # line)
which_analysis()
-# """
-# Tool rules ---------------------------------------------------------------------------------------
-# """
-# rule samtools_index:
-# # Samtools faidx to index compressed fasta
-# input:
-# fa="{sample}.fa.gz"
-# output:
-# "{sample}.fa.gz.fai",
-# "{sample}.fa.gz.gzi"
-# threads: 1
-# params:
-# app_path=config["app.path"]
-# shell:
-# "apptainer run --app samtools {params.app_path}/PanGeTools.sif "
-# "faidx {input.fa}"
-
"""
Pre-processing section : preparing pggb inputs ---------------------------------------------------
"""
@@ -285,471 +266,475 @@ rule create_sglAsm_syri_fig:
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
"""
-# """
-# Core section : Running PGGB
-# """
-
-# rule create_pggb_input_syri_fig:
-# input:
-# fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
-# output:
-# fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
-# wrkdir=directory('data/chrInput/syri/{chromosome}')
-# threads: 8
-# params:
-# app_path=config["app.path"],
-# ref=config['reference']
-# shell:
-# """
-# mkdir {output.wrkdir}
-# refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
-
-# ## Creating single fasta from multifasta
-# zcat {input.fasta} | awk -F"#" \
-# '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
+"""
+
+Core section : Running PGGB
+
+"""
+
+rule create_pggb_input_syri_fig:
+ input:
+ fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
+ output:
+ fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
+ wrkdir=directory('data/chrInput/syri/{chromosome}')
+ threads: 8
+ params:
+ app_path=config["app.path"],
+ ref=config['reference']
+ shell:
+ """
+ mkdir {output.wrkdir}
+ refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
+
+ ## Creating single fasta from multifasta
+ zcat {input.fasta} | awk -F"#" \
+ '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
-# ## Getting the list of sequences
-# asmList=()
-# for file in {output.wrkdir}/*.fa; do
-# asm="$(basename $file .fa | cut -f1 -d"#").fa"
-# mv $file "$(dirname $file)/$asm"
-# asmList+=("$asm")
-# done
-
-# bash scripts/getSyriFigs.sh \
-# -a {params.app_path} \
-# -t {threads} \
-# -d {output.wrkdir} \
-# -o $(basename {output.fig}) \
-# -r {output.wrkdir}/"${refname}.fa" \
-# -q "${asmList[@]}"
-# mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
-# rm {output.wrkdir}/*.fa
-# """
-
-# rule wfmash_on_chr:
-# # Run wfmash on a specific chromosome input
-# input:
-# fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
-# fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
-# output:
-# mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
-# aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
-# threads: 16
-# params:
-# app_path=config['app.path'],
-# segment_length=config['wfmash.segment_length'],
-# mapping_id=config['wfmash.mapping_id'],
-# wfmash_sec=config['wfmash.secondary']
-# log:
-# cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
-# time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
-# cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
-# time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
-# shell:
-# """
-# ## Mapping
-# /usr/bin/time -v -o {log.time_map} \
-# apptainer exec {params.app_path}/pggb.sif wfmash \
-# -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
-# -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
-# --tmp-base $(dirname {output.aln}) \
-# {input.fa} --approx-map \
-# 1> {output.mapping} \
-# 2> >(tee {log.cmd_map} >&2)
-
-# ## Aligning
-# /usr/bin/time -v -o {log.time_aln} \
-# apptainer exec {params.app_path}/pggb.sif wfmash \
-# -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
-# -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
-# --tmp-base $(dirname {output.aln}) \
-# {input.fa} -i {output.mapping} \
-# --invert-filtering \
-# 1> {output.aln} \
-# 2> >(tee {log.cmd_aln} >&2)
-
-# # Compressing
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} -k {output.mapping}
-
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} -k {output.aln}
-# """
-
-# rule seqwish:
-# # Run seqwish on alignement produced by wfmash
-# input:
-# fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
-# aln=rules.wfmash_on_chr.output.aln
-# output:
-# temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
-# threads: 8
-# params:
-# app_path=config['app.path'],
-# seqwish=config['seqwish.params']
-# log:
-# cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
-# time="logs/pggb/{chromosome}.seqwish.time.log"
-# shell:
-# """
-# /usr/bin/time -v -o {log.time} \
-# apptainer exec {params.app_path}/pggb.sif seqwish \
-# -s {input.fa} -p {input.aln} -g {output} \
-# {params.seqwish} -t {threads} \
-# --temp-dir $(dirname {output}) -P 2>&1 | \
-# tee {log.cmd}
-
-# # Compressing
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} -k {output}
-# """
-
-# rule gfaffix_on_chr:
-# # Run gfaffix on seqwish graph
-# input:
-# rules.seqwish.output
-# output:
-# gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
-# transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
-# threads: 1
-# params:
-# app_path=config['app.path']
-# log:
-# time="logs/pggb/{chromosome}.gfaffix.time.log"
-# shell:
-# """
-# /usr/bin/time -v -o {log.time} \
-# apptainer exec {params.app_path}/pggb.sif gfaffix \
-# {input} -o {output.gfa} -t {output.transform} \
-# > /dev/null
-
-# # Compressing
-# apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# -@ {threads} -k {output.gfa}
-# """
-
-# rule odgi_postprocessing:
-# # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
-# input:
-# rules.gfaffix_on_chr.output.gfa
-# output:
-# gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
-# threads: 8
-# params:
-# app_path=config['app.path']
-# log:
-# cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
-# time_build="logs/pggb/{chromosome}.odgi_build.time.log",
-# cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
-# time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
-# cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
-# time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
-# cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
-# time_view="logs/pggb/{chromosome}.odgi_view.time.log"
-# shell:
-# """
-# OGfile="$(dirname {input})/$(basename {input} .gfa)"
-
-# ## Converting to odgi format and optimizing namespace
-# /usr/bin/time -v -o {log.time_build} \
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
-# tee {log.cmd_build}
+ ## Getting the list of sequences
+ asmList=()
+ for file in {output.wrkdir}/*.fa; do
+ asm="$(basename $file .fa | cut -f1 -d"#").fa"
+ mv $file "$(dirname $file)/$asm"
+ asmList+=("$asm")
+ done
+
+ bash scripts/getSyriFigs.sh \
+ -a {params.app_path} \
+ -t {threads} \
+ -d {output.wrkdir} \
+ -o $(basename {output.fig}) \
+ -r {output.wrkdir}/"${refname}.fa" \
+ -q "${asmList[@]}"
+ mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
+ rm {output.wrkdir}/*.fa
+ """
+
+rule wfmash_on_chr:
+ # Run wfmash on a specific chromosome input
+ input:
+ fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+ fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
+ output:
+ mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
+ aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
+ threads: 16
+ params:
+ app_path=config['app.path'],
+ segment_length=config['wfmash.segment_length'],
+ mapping_id=config['wfmash.mapping_id'],
+ wfmash_sec=config['wfmash.secondary']
+ log:
+ cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
+ time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
+ cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
+ time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
+ shell:
+ """
+ ## Mapping
+ /usr/bin/time -v -o {log.time_map} \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} --approx-map \
+ 1> {output.mapping} \
+ 2> >(tee {log.cmd_map} >&2)
+
+ ## Aligning
+ /usr/bin/time -v -o {log.time_aln} \
+ apptainer exec {params.app_path}/pggb.sif wfmash \
+ -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
+ -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
+ --tmp-base $(dirname {output.aln}) \
+ {input.fa} -i {output.mapping} \
+ --invert-filtering \
+ 1> {output.aln} \
+ 2> >(tee {log.cmd_aln} >&2)
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.mapping}
+
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.aln}
+ """
+
+rule seqwish:
+ # Run seqwish on alignement produced by wfmash
+ input:
+ fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
+ aln=rules.wfmash_on_chr.output.aln
+ output:
+ temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
+ threads: 8
+ params:
+ app_path=config['app.path'],
+ seqwish=config['seqwish.params']
+ log:
+ cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
+ time="logs/pggb/{chromosome}.seqwish.time.log"
+ shell:
+ """
+ /usr/bin/time -v -o {log.time} \
+ apptainer exec {params.app_path}/pggb.sif seqwish \
+ -s {input.fa} -p {input.aln} -g {output} \
+ {params.seqwish} -t {threads} \
+ --temp-dir $(dirname {output}) -P 2>&1 | \
+ tee {log.cmd}
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output}
+ """
+
+rule gfaffix_on_chr:
+ # Run gfaffix on seqwish graph
+ input:
+ rules.seqwish.output
+ output:
+ gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
+ transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
+ threads: 1
+ params:
+ app_path=config['app.path']
+ log:
+ time="logs/pggb/{chromosome}.gfaffix.time.log"
+ shell:
+ """
+ /usr/bin/time -v -o {log.time} \
+ apptainer exec {params.app_path}/pggb.sif gfaffix \
+ {input} -o {output.gfa} -t {output.transform} \
+ > /dev/null
+
+ # Compressing
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} -k {output.gfa}
+ """
+
+rule odgi_postprocessing:
+ # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
+ input:
+ rules.gfaffix_on_chr.output.gfa
+ output:
+ gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ threads: 8
+ params:
+ app_path=config['app.path']
+ log:
+ cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
+ time_build="logs/pggb/{chromosome}.odgi_build.time.log",
+ cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
+ time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
+ cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
+ time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
+ cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
+ time_view="logs/pggb/{chromosome}.odgi_view.time.log"
+ shell:
+ """
+ OGfile="$(dirname {input})/$(basename {input} .gfa)"
+
+ ## Converting to odgi format and optimizing namespace
+ /usr/bin/time -v -o {log.time_build} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
+ tee {log.cmd_build}
-# ## Unchoping the nodes (merges unitigs into single nodes)
-# /usr/bin/time -v -o {log.time_unchop} \
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
-# tee {log.cmd_unchop}
-
-# ## Sorting the nodes
-# /usr/bin/time -v -o {log.time_sort} \
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
-# -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
-# tee {log.cmd_sort}
-
-# ## Exporting to gfa
-# /usr/bin/time -v -o {log.time_view} \
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# view -i $OGfile.unchoped.sorted.og -g \
-# 1> {output.gfa} \
-# 2> >(tee {log.cmd_view} >&2)
-
-# ## Removing .og files for space savings
-# rm $(dirname {input})/*.og
-
-# ## Adding metadata
-# python scripts/getTags.py \
-# --appdir {params.app_path} --config-file config.yaml \
-# > "$(dirname {input})/metadata.txt"
-# sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
-
-# # Compressing
-# # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-# # -@ {threads} -k {output.gfa}
-# """
-
-# rule generate_graph_list:
-# # Generate a text file containing all created graphs
-# input:
-# expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
-# output:
-# "data/chrGraphs/graphsList.txt"
-# threads: 1
-# run:
-# with open(output[0], "w") as handle:
-# for file in input:
-# handle.write(file+"\n")
-
-# rule graph_squeeze:
-# # Using odgi to merge every subgraphs into a final one
-# input:
-# glist="data/chrGraphs/graphsList.txt",
-# graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
-# output:
-# "output/pan1c."+config['name']+".gfa"
-# threads: 16
-# params:
-# app_path=config['app.path']
-# shell:
-# """
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# view -t {threads} -P -i {output}.og -g > {output}
-# rm {output}.og
-# """
-
-# rule graph_stats:
-# # Using GFAstats to produce stats on every chromosome graphs
-# input:
-# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
-# output:
-# genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
-# pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
-# threads: 4
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name']
-# shell:
-# """
-# apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
-# -g {input.graph} -P \
-# -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
-# -t {threads}
-# """
-
-# rule graph_figs:
-# # Creating figures using odgi viz
-# input:
-# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
-# output:
-# oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
-# pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
-# threads: 4
-# params:
-# app_path=config['app.path'],
-# oneDviz=config['odgi.1Dviz.params'],
-# pcov=config['odgi.pcov.params']
-# shell:
-# """
-# ## 1D viz
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
-
-# ## Pcov viz
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
-# """
-
-# rule aggregate_graphs_stats:
-# # Reading and merging all stats files from chromosome graphs into a .tsv.
-# input:
-# genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
-# output:
-# genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
-# pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name']
-# shell:
-# """
-# apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
-# --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
-# --outputPaths {output.pathstats} --panname {params.pan_name}
-# """
-
-# rule final_graph_tagging:
-# # Add metadata to the final GFA
-# input:
-# graph="output/pan1c."+config['name']+".gfa",
-# output:
-# "output/pan1c."+config['name']+".gfa.metadata"
-# threads: 1
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name']
-# shell:
-# """
-# python scripts/getTags.py \
-# --appdir {params.app_path} --config-file config.yaml > {output}
-# sed -i '/^H/r {output}' {input.graph}
-# """
-
-# rule pggb_input_stats:
-# # Produces statistics on pggb input sequences
-# input:
-# flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
-# output:
-# "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name']
-# shell:
-# """
-# apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
-# -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
-# """
-
-# rule core_statistics:
-# # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
-# input:
-# chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
-# chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
-# output:
-# tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
-# dir=directory("output/pggb.usage.figs")
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name']
-# shell:
-# """
-# mkdir -p {output.dir}
-# apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
-# --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
-# --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
-# """
-
-# """
-# Post-processing section :
-# The graph for each chromosome are made as well as some basic statistics.
-# In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
-# It also contains rules to use the graph itself.
-# """
-# rule get_pav:
-# # Create PAV matrix readable by panache for a given chromosome scale graph
-# input:
-# "data/chrGraphs/graphsList.txt"
-# output:
-# directory("output/pav.matrices")
-# threads: 16
-# params:
-# app_path=config['app.path']
-# run:
-# shell("mkdir {output}")
-# # Getting the list of graphs
-# with open(input[0]) as handle:
-# graphList = [graph.rstrip("\n") for graph in handle.readlines()]
-# # Iterating over graphs
-# for graph in graphList:
-# shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
-
-# rule panacus_stats:
-# # Produces panacus reports for a chromosome graph
-# input:
-# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
-# output:
-# html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
-# params:
-# app_path=config['app.path'],
-# pan_name=config['name'],
-# refname=config['reference']
-# threads: 8
-# shell:
-# """
-# bash scripts/getPanacusHG.sh \
-# -g {input.graph} \
-# -r $(basename {params.refname} .fa.gz) \
-# -d data/chrGraphs/{wildcards.chromosome} \
-# -o {output.html} \
-# -a {params.app_path} \
-# -t {threads}
-# """
-
-# rule create_pan1c_report_fig:
-# # Produces a markdown report figure of chromosomes graphs
-# input:
-# graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
-# contigfig="output/chr.contig/{chromosome}.contig.png",
-# output:
-# odgifig=temp("tmp/{chromosome}.odgi.png"),
-# namefig=temp("tmp/{chromosome}.name.png"),
-# reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
-# threads: 4
-# params:
-# app_path=config['app.path']
-# shell:
-# """
-# ## Odgi 1D viz
-# apptainer run --app odgi {params.app_path}/PanGeTools.sif \
-# viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
-
-# ## Getting legend from contig figure
-# convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
-
-# odgheight=$(identify -ping -format '%h' {output.odgifig})
-# ctgheight=$(identify -ping -format '%h' {input.contigfig})
-
-# combinedheight=$(($odgheight+$ctgheight))
-
-# echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
-
-# ## Creating empty canvas ad adding other figures to it
-# convert -size "3300x$combinedheight" xc:white {output.reportfig}
-# composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
-# composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
-# composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
-# """
-
-# rule create_pan1c_report:
-# # Produces a markdown report of chromosomes graphs
-# input:
-# figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
-# genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
-# pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
-# output:
-# reportfig="output/pan1c."+config['name']+".report.md"
-# threads: 4
-# params:
-# app_path=config['app.path']
-# run:
-# shell("touch {output.reportfig}")
-
-# # Adding Summary
-# ## To Do
-
-# # Adding General stats
-# shell("echo '# General stats' >> {output.reportfig}")
-# shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
-# shell("echo '' >> {output.reportfig}")
-
-# # Adding Path stats
-# shell("echo '# Path stats' >> {output.reportfig}")
-# shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
-# shell("echo '' >> {output.reportfig}")
-
-# # Adding chromosomes figures
-# fig_list = [fig for fig in input.figs]
-# print(fig_list)
-# fig_list.sort()
+ ## Unchoping the nodes (merges unitigs into single nodes)
+ /usr/bin/time -v -o {log.time_unchop} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
+ tee {log.cmd_unchop}
+
+ ## Sorting the nodes
+ /usr/bin/time -v -o {log.time_sort} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
+ -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
+ tee {log.cmd_sort}
+
+ ## Exporting to gfa
+ /usr/bin/time -v -o {log.time_view} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ view -i $OGfile.unchoped.sorted.og -g \
+ 1> {output.gfa} \
+ 2> >(tee {log.cmd_view} >&2)
+
+ ## Removing .og files for space savings
+ rm $(dirname {input})/*.og
+
+ ## Adding metadata
+ python scripts/getTags.py \
+ --appdir {params.app_path} --config-file config.yaml \
+ > "$(dirname {input})/metadata.txt"
+ sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
+
+ # Compressing
+ # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ # -@ {threads} -k {output.gfa}
+ """
+
+rule generate_graph_list:
+ # Generate a text file containing all created graphs
+ input:
+ expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+ output:
+ "data/chrGraphs/graphsList.txt"
+ threads: 1
+ run:
+ with open(output[0], "w") as handle:
+ for file in input:
+ handle.write(file+"\n")
+
+rule graph_squeeze:
+ # Using odgi to merge every subgraphs into a final one
+ input:
+ glist="data/chrGraphs/graphsList.txt",
+ graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
+ output:
+ "output/pan1c."+config['name']+".gfa"
+ threads: 16
+ params:
+ app_path=config['app.path']
+ shell:
+ """
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ view -t {threads} -P -i {output}.og -g > {output}
+ rm {output}.og
+ """
+
+rule graph_stats:
+ # Using GFAstats to produce stats on every chromosome graphs
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
+ pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
+ threads: 4
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
+ -g {input.graph} -P \
+ -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
+ -t {threads}
+ """
+
+rule graph_figs:
+ # Creating figures using odgi viz
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
+ pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
+ threads: 4
+ params:
+ app_path=config['app.path'],
+ oneDviz=config['odgi.1Dviz.params'],
+ pcov=config['odgi.pcov.params']
+ shell:
+ """
+ ## 1D viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
+
+ ## Pcov viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
+ """
+
+rule aggregate_graphs_stats:
+ # Reading and merging all stats files from chromosome graphs into a .tsv.
+ input:
+ genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
+ output:
+ genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
+ --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
+ --outputPaths {output.pathstats} --panname {params.pan_name}
+ """
+
+rule final_graph_tagging:
+ # Add metadata to the final GFA
+ input:
+ graph="output/pan1c."+config['name']+".gfa",
+ output:
+ "output/pan1c."+config['name']+".gfa.metadata"
+ threads: 1
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ python scripts/getTags.py \
+ --appdir {params.app_path} --config-file config.yaml > {output}
+ sed -i '/^H/r {output}' {input.graph}
+ """
+
+rule pggb_input_stats:
+ # Produces statistics on pggb input sequences
+ input:
+ flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ output:
+ "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
+ -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
+ """
+
+rule core_statistics:
+ # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
+ input:
+ chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
+ chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ output:
+ tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
+ dir=directory("output/pggb.usage.figs")
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name']
+ shell:
+ """
+ mkdir -p {output.dir}
+ apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
+ --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
+ --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
+ """
+
+"""
+
+Post-processing section :
+ The graph for each chromosome are made as well as some basic statistics.
+ In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
+ It also contains rules to use the graph itself.
+
+"""
+rule get_pav:
+ # Create PAV matrix readable by panache for a given chromosome scale graph
+ input:
+ "data/chrGraphs/graphsList.txt"
+ output:
+ directory("output/pav.matrices")
+ threads: 16
+ params:
+ app_path=config['app.path']
+ run:
+ shell("mkdir {output}")
+ # Getting the list of graphs
+ with open(input[0]) as handle:
+ graphList = [graph.rstrip("\n") for graph in handle.readlines()]
+ # Iterating over graphs
+ for graph in graphList:
+ shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
+
+rule panacus_stats:
+ # Produces panacus reports for a chromosome graph
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
+ output:
+ html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
+ params:
+ app_path=config['app.path'],
+ pan_name=config['name'],
+ refname=config['reference']
+ threads: 8
+ shell:
+ """
+ bash scripts/getPanacusHG.sh \
+ -g {input.graph} \
+ -r $(basename {params.refname} .fa.gz) \
+ -d data/chrGraphs/{wildcards.chromosome} \
+ -o {output.html} \
+ -a {params.app_path} \
+ -t {threads}
+ """
+
+rule create_pan1c_report_fig:
+ # Produces a markdown report figure of chromosomes graphs
+ input:
+ graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
+ contigfig="output/chr.contig/{chromosome}.contig.png",
+ output:
+ odgifig=temp("tmp/{chromosome}.odgi.png"),
+ namefig=temp("tmp/{chromosome}.name.png"),
+ reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
+ threads: 4
+ params:
+ app_path=config['app.path']
+ shell:
+ """
+ ## Odgi 1D viz
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
+
+ ## Getting legend from contig figure
+ convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
+
+ odgheight=$(identify -ping -format '%h' {output.odgifig})
+ ctgheight=$(identify -ping -format '%h' {input.contigfig})
+
+ combinedheight=$(($odgheight+$ctgheight))
+
+ echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
+
+ ## Creating empty canvas ad adding other figures to it
+ convert -size "3300x$combinedheight" xc:white {output.reportfig}
+ composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
+ composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
+ composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
+ """
+
+rule create_pan1c_report:
+ # Produces a markdown report of chromosomes graphs
+ input:
+ figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
+ genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ output:
+ reportfig="output/pan1c."+config['name']+".report.md"
+ threads: 4
+ params:
+ app_path=config['app.path']
+ run:
+ shell("touch {output.reportfig}")
+
+ # Adding Summary
+ ## To Do
+
+ # Adding General stats
+ shell("echo '# General stats' >> {output.reportfig}")
+ shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding Path stats
+ shell("echo '# Path stats' >> {output.reportfig}")
+ shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+
+ # Adding chromosomes figures
+ fig_list = [fig for fig in input.figs]
+ print(fig_list)
+ fig_list.sort()
-# shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
-# for fig in fig_list:
-# basename=os.path.basename(fig)
-# chr_name=basename.split('.')[1]
+ shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
+ for fig in fig_list:
+ basename=os.path.basename(fig)
+ chr_name=basename.split('.')[1]
-# shell("echo '## {chr_name}' >> {output.reportfig}")
-# shell("echo '' >> {output.reportfig}")
-# shell("echo '' >> {output.reportfig}")
\ No newline at end of file
+ shell("echo '## {chr_name}' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
+ shell("echo '' >> {output.reportfig}")
\ No newline at end of file
diff --git a/rules/core.smk b/rules/core.smk
deleted file mode 100644
index 5473943..0000000
--- a/rules/core.smk
+++ /dev/null
@@ -1,346 +0,0 @@
-"""
-Core section : Running PGGB on each chromosome and generating whole pangenome -------------------
-"""
-
-rule create_pggb_input_syri_fig:
- input:
- fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
- output:
- fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
- wrkdir=directory('data/chrInput/syri/{chromosome}')
- threads: 8
- params:
- app_path=config["app.path"],
- ref=config['reference']
- shell:
- """
- mkdir {output.wrkdir}
- refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
-
- ## Creating single fasta from multifasta
- zcat {input.fasta} | awk -F"#" \
- '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
-
- ## Getting the list of sequences
- asmList=()
- for file in {output.wrkdir}/*.fa; do
- asm="$(basename $file .fa | cut -f1 -d"#").fa"
- mv $file "$(dirname $file)/$asm"
- asmList+=("$asm")
- done
-
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {output.wrkdir}/"${refname}.fa" \
- -q "${asmList[@]}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- rm {output.wrkdir}/*.fa
- """
-
-rule wfmash_on_chr:
- # Run wfmash on a specific chromosome input
- input:
- fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
- fai='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz.fai'
- output:
- mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
- aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
- threads: 16
- params:
- app_path=config['app.path'],
- segment_length=config['wfmash.segment_length'],
- mapping_id=config['wfmash.mapping_id'],
- wfmash_sec=config['wfmash.secondary']
- log:
- cmd_map="logs/pggb/{chromosome}.wfmash_mapping.cmd.log",
- time_map="logs/pggb/{chromosome}.wfmash_mapping.time.log",
- cmd_aln="logs/pggb/{chromosome}.wfmash_aln.cmd.log",
- time_aln="logs/pggb/{chromosome}.wfmash_aln.time.log",
- shell:
- """
- ## Mapping
- /usr/bin/time -v -o {log.time_map} \
- apptainer exec {params.app_path}/pggb.sif wfmash \
- -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
- -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
- --tmp-base $(dirname {output.aln}) \
- {input.fa} --approx-map \
- 1> {output.mapping} \
- 2> >(tee {log.cmd_map} >&2)
-
- ## Aligning
- /usr/bin/time -v -o {log.time_aln} \
- apptainer exec {params.app_path}/pggb.sif wfmash \
- -s {params.segment_length} -l $(( {params.segment_length} * 5 )) -p {params.mapping_id} \
- -n $(cat {input.fai} | wc -l) {params.wfmash_sec} -t {threads} \
- --tmp-base $(dirname {output.aln}) \
- {input.fa} -i {output.mapping} \
- --invert-filtering \
- 1> {output.aln} \
- 2> >(tee {log.cmd_aln} >&2)
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.mapping}
-
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.aln}
- """
-
-rule seqwish:
- # Run seqwish on alignement produced by wfmash
- input:
- fa='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz',
- aln=rules.wfmash_on_chr.output.aln
- output:
- temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
- threads: 8
- params:
- app_path=config['app.path'],
- seqwish=config['seqwish.params']
- log:
- cmd="logs/pggb/{chromosome}.seqwish.cmd.log",
- time="logs/pggb/{chromosome}.seqwish.time.log"
- shell:
- """
- /usr/bin/time -v -o {log.time} \
- apptainer exec {params.app_path}/pggb.sif seqwish \
- -s {input.fa} -p {input.aln} -g {output} \
- {params.seqwish} -t {threads} \
- --temp-dir $(dirname {output}) -P 2>&1 | \
- tee {log.cmd}
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output}
- """
-
-rule gfaffix_on_chr:
- # Run gfaffix on seqwish graph
- input:
- rules.seqwish.output
- output:
- gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
- transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
- threads: 1
- params:
- app_path=config['app.path']
- log:
- time="logs/pggb/{chromosome}.gfaffix.time.log"
- shell:
- """
- /usr/bin/time -v -o {log.time} \
- apptainer exec {params.app_path}/pggb.sif gfaffix \
- {input} -o {output.gfa} -t {output.transform} \
- > /dev/null
-
- # Compressing
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} -k {output.gfa}
- """
-
-rule odgi_postprocessing:
- # Running pggb's postprocessing (mainly odgi) steps with gfaffix graph
- input:
- rules.gfaffix_on_chr.output.gfa
- output:
- gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- threads: 8
- params:
- app_path=config['app.path']
- log:
- cmd_build="logs/pggb/{chromosome}.odgi_build.cmd.log",
- time_build="logs/pggb/{chromosome}.odgi_build.time.log",
- cmd_unchop="logs/pggb/{chromosome}.odgi_unchop.cmd.log",
- time_unchop="logs/pggb/{chromosome}.odgi_unchop.time.log",
- cmd_sort="logs/pggb/{chromosome}.odgi_sort.cmd.log",
- time_sort="logs/pggb/{chromosome}.odgi_sort.time.log",
- cmd_view="logs/pggb/{chromosome}.odgi_view.cmd.log",
- time_view="logs/pggb/{chromosome}.odgi_view.time.log"
- shell:
- """
- OGfile="$(dirname {input})/$(basename {input} .gfa)"
-
- ## Converting to odgi format and optimizing namespace
- /usr/bin/time -v -o {log.time_build} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- build -t {threads} -P -g {input} -o $OGfile.og -O 2>&1 | \
- tee {log.cmd_build}
-
- ## Unchoping the nodes (merges unitigs into single nodes)
- /usr/bin/time -v -o {log.time_unchop} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- unchop -P -t {threads} -i $OGfile.og -o $OGfile.unchoped.og 2>&1 | \
- tee {log.cmd_unchop}
-
- ## Sorting the nodes
- /usr/bin/time -v -o {log.time_sort} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- sort -P -p Ygs --temp-dir $(dirname $OGfile) -t {threads} \
- -i $OGfile.unchoped.og -o $OGfile.unchoped.sorted.og 2>&1 | \
- tee {log.cmd_sort}
-
- ## Exporting to gfa
- /usr/bin/time -v -o {log.time_view} \
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- view -i $OGfile.unchoped.sorted.og -g \
- 1> {output.gfa} \
- 2> >(tee {log.cmd_view} >&2)
-
- ## Removing .og files for space savings
- rm $(dirname {input})/*.og
-
- ## Adding metadata
- python scripts/getTags.py \
- --appdir {params.app_path} --config-file config.yaml \
- > "$(dirname {input})/metadata.txt"
- sed -i "/^H/r $(dirname {input})/metadata.txt" {output.gfa}
-
- # Compressing
- # apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- # -@ {threads} -k {output.gfa}
- """
-
-rule generate_graph_list:
- # Generate a text file containing all created graphs
- input:
- expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
- output:
- "data/chrGraphs/graphsList.txt"
- threads: 1
- run:
- with open(output[0], "w") as handle:
- for file in input:
- handle.write(file+"\n")
-
-rule graph_squeeze:
- # Using odgi to merge every subgraphs into a final one
- input:
- glist="data/chrGraphs/graphsList.txt",
- graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
- output:
- "output/pan1c."+config['name']+".gfa"
- threads: 16
- params:
- app_path=config['app.path']
- shell:
- """
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- view -t {threads} -P -i {output}.og -g > {output}
- rm {output}.og
- """
-
-rule graph_stats:
- # Using GFAstats to produce stats on every chromosome graphs
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- genstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv",
- pathstats="output/stats/chrGraphs/"+config['name']+".{chromosome}.path.stats.tsv"
- threads: 4
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run --app gfastats {params.app_path}/PanGeTools.sif \
- -g {input.graph} -P \
- -o $(dirname {output.genstats})/{params.pan_name}.{wildcards.chromosome} \
- -t {threads}
- """
-
-rule graph_figs:
- # Creating figures using odgi viz
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- oneDviz="output/chrGraphs.figs/"+config['name']+".{chromosome}.1Dviz.png",
- pcov="output/chrGraphs.figs/"+config['name']+".{chromosome}.pcov.png"
- threads: 4
- params:
- app_path=config['app.path'],
- oneDviz=config['odgi.1Dviz.params'],
- pcov=config['odgi.pcov.params']
- shell:
- """
- ## 1D viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.oneDviz} {params.oneDviz} -t {threads} -P
-
- ## Pcov viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.pcov} {params.pcov} -t {threads} -P
- """
-
-rule aggregate_graphs_stats:
- # Reading and merging all stats files from chromosome graphs into a .tsv.
- input:
- genstats=expand("output/stats/chrGraphs/"+config['name']+".{chromosome}.general.stats.tsv", chromosome=CHRLIST)
- output:
- genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif python scripts/chrStatsAggregation.py \
- --input $(dirname {input[0]}) --outputGeneral {output.genstats} \
- --outputPaths {output.pathstats} --panname {params.pan_name}
- """
-
-rule final_graph_tagging:
- # Add metadata to the final GFA
- input:
- graph="output/pan1c."+config['name']+".gfa",
- output:
- "output/pan1c."+config['name']+".gfa.metadata"
- threads: 1
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- python scripts/getTags.py \
- --appdir {params.app_path} --config-file config.yaml > {output}
- sed -i '/^H/r {output}' {input.graph}
- """
-
-rule pggb_input_stats:
- # Produces statistics on pggb input sequences
- input:
- flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
- output:
- "output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif python scripts/chrInputStats.py \
- -f data/chrInputs/*.fa.gz -o {output} -p {params.pan_name}
- """
-
-rule core_statistics:
- # Aggregate chrInput, chrGraph and pggb statistics into a single tsv
- input:
- chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
- chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
- output:
- tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
- dir=directory("output/pggb.usage.figs")
- params:
- app_path=config['app.path'],
- pan_name=config['name']
- shell:
- """
- mkdir -p {output.dir}
- apptainer run {params.app_path}/pan1c-env.sif python scripts/coreStats.py \
- --pggbStats logs/pggb --chrInputStats {input.chrInputStats} \
- --chrGraphStats {input.chrGraphStats} -o {output.tsv} -f {output.dir} -p {params.pan_name}
- """
\ No newline at end of file
diff --git a/rules/post-analysis.smk b/rules/post-analysis.smk
deleted file mode 100644
index 3041501..0000000
--- a/rules/post-analysis.smk
+++ /dev/null
@@ -1,118 +0,0 @@
-"""
-Post-analysis section ---------------------------------------------------------------------------
-"""
-rule get_pav:
- # Create PAV matrix readable by panache for a given chromosome scale graph
- input:
- "data/chrGraphs/graphsList.txt"
- output:
- directory("output/pav.matrices")
- threads: 16
- params:
- app_path=config['app.path']
- run:
- shell("mkdir {output}")
- # Getting the list of graphs
- with open(input[0]) as handle:
- graphList = [graph.rstrip("\n") for graph in handle.readlines()]
- # Iterating over graphs
- for graph in graphList:
- shell("bash scripts/getPanachePAV.sh -g {graph} -d data/chrGraphs/$(basename {graph} .gfa) -o {output}/$(basename {graph} .gfa).pav.matrix.tsv -a {params.app_path} -t {threads}")
-
-rule panacus_stats:
- # Produces panacus reports for a chromosome graph
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
- output:
- html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
- params:
- app_path=config['app.path'],
- pan_name=config['name'],
- refname=config['reference']
- threads: 8
- shell:
- """
- bash scripts/getPanacusHG.sh \
- -g {input.graph} \
- -r $(basename {params.refname} .fa.gz) \
- -d data/chrGraphs/{wildcards.chromosome} \
- -o {output.html} \
- -a {params.app_path} \
- -t {threads}
- """
-
-rule create_pan1c_report_fig:
- # Produces a markdown report figure of chromosomes graphs
- input:
- graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa',
- contigfig="output/chr.contig/{chromosome}.contig.png",
- output:
- odgifig=temp("tmp/{chromosome}.odgi.png"),
- namefig=temp("tmp/{chromosome}.name.png"),
- reportfig="output/report/"+config['name']+".{chromosome}.report.fig.png"
- threads: 4
- params:
- app_path=config['app.path']
- shell:
- """
- ## Odgi 1D viz
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- viz -i {input.graph} -o {output.odgifig} -x 2500 -a 80 -b -H -t {threads} -P
-
- ## Getting legend from contig figure
- convert {input.contigfig} -crop 790x+0+0 +repage {output.namefig}
-
- odgheight=$(identify -ping -format '%h' {output.odgifig})
- ctgheight=$(identify -ping -format '%h' {input.contigfig})
-
- combinedheight=$(($odgheight+$ctgheight))
-
- echo -e "[Debug::Report fig]\t$odgheight\t$ctgheight\t$combinedheight"
-
- ## Creating empty canvas ad adding other figures to it
- convert -size "3300x$combinedheight" xc:white {output.reportfig}
- composite -geometry +0+0 {input.contigfig} {output.reportfig} {output.reportfig}
- composite -geometry "+0+$ctgheight" {output.namefig} {output.reportfig} {output.reportfig}
- composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
- """
-
-rule create_pan1c_report:
- # Produces a markdown report of chromosomes graphs
- input:
- figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
- genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
- output:
- reportfig="output/pan1c."+config['name']+".report.md"
- threads: 4
- params:
- app_path=config['app.path']
- run:
- shell("touch {output.reportfig}")
-
- # Adding Summary
- ## To Do
-
- # Adding General stats
- shell("echo '# General stats' >> {output.reportfig}")
- shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
-
- # Adding Path stats
- shell("echo '# Path stats' >> {output.reportfig}")
- shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
-
- # Adding chromosomes figures
- fig_list = [fig for fig in input.figs]
- print(fig_list)
- fig_list.sort()
-
- shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
- for fig in fig_list:
- basename=os.path.basename(fig)
- chr_name=basename.split('.')[1]
-
- shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
\ No newline at end of file
diff --git a/rules/pre-processing.smk b/rules/pre-processing.smk
deleted file mode 100644
index 3580108..0000000
--- a/rules/pre-processing.smk
+++ /dev/null
@@ -1,185 +0,0 @@
-"""
-Pre-processing section : preparing haplotypes ----------------------------------------------------
-"""
-rule ragtag_scaffolding:
- # Scaffold input haplotype against the reference to infer chromosome scale sequences
- input:
- ref="data/haplotypes/"+config['reference'],
- reffai="data/haplotypes/"+config['reference']+".fai",
- refgzi="data/haplotypes/"+config['reference']+".gzi",
- fa="data/haplotypes/{haplotype}.fa.gz"
- output:
- fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
- tar="data/hap.ragtagged/{haplotype}.tar.gz"
- threads: 8
- retries: 1
- params:
- app_path=config["app.path"]
- shell:
- """
- bash scripts/ragtagChromInfer.sh \
- -d $(dirname {output.fa})/{wildcards.haplotype} \
- -a {params.app_path} \
- -t {threads} \
- -r {input.ref} \
- -q {input.fa} \
- -o {output.fa}
-
- #if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
- # echo "Error : Empty final fasta"
- # exit 1
- #fi
- """
-
-rule quast_stats:
- # Run Quast on ragtagged genomes
- input:
- fas=expand("data/haplotypes/{haplotype}.fa.gz", haplotype=SAMPLES_NOREF),
- ref="data/haplotypes/"+config['reference']
- output:
- report="output/quast/"+config['name']+".quast.report.html"
- threads: 8
- params:
- app_path=config["app.path"],
- pan_name=config["name"]
- shell:
- """
- apptainer run {params.app_path}/pan1c-env.sif quast.py \
- -t {threads} \
- -o "$(dirname {output.report})" \
- -r {input.ref} \
- --plots-format png \
- --no-read-stats \
- --no-icarus \
- -s \
- --large \
- {input.fas}
-
- # Compressing temporary files
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} $(dirname {output.report})/contigs_reports/*.fa
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads} $(dirname {output.report})/contigs_reports/minimap_output/*
-
- mv $(dirname {output.report})/report.html {output.report}
- """
-
-rule contig_position:
- # Produce figures with contig positions
- input:
- fa="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz",
- fai="data/chrInputs/"+config["name"]+".{chromosome}.fa.gz.fai"
- output:
- fig="output/chr.contig/{chromosome}.contig.png",
- outdir=directory("output/chr.contig/{chromosome}")
- threads: 1
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir {output.outdir}
- base="{output.outdir}"
- hapID=$(echo {wildcards.chromosome} | sed 's/.hap/#/')
-
- # Creating .bands file
- apptainer run {params.app_path}/pan1c-env.sif python scripts/fasta_not_NNN_gff3.py \
- -s 5 \
- -f {input.fa} \
- > $base/{wildcards.chromosome}.gff
-
- #cat $base/{wildcards.chromosome}.gff
-
- awk '{{a++; if ((a/2)==int(a/2)){{b="gpos25"}}else{{b="gpos75"}}; print $1"\\t"$4"\\t"$5"\\tcontig_"a"\\t"b}}' $base/{wildcards.chromosome}.gff | \
- sed '1ichr\\tstart\\tend\\tname\\tgieStain' \
- > $base/{wildcards.chromosome}.bands
-
- #cat $base/{wildcards.chromosome}.bands
-
- # Creating bed like file
- cat {input.fai} | \
- cut -f1,2 | tr '\\t' ',' | \
- sed "s/,/,1,/" | \
- sed "1i chr\\tstart\\tend" | \
- tr ',' '\\t' \
- > $base/{wildcards.chromosome}.tsv
-
- #cat $base/{wildcards.chromosome}.tsv
-
- # Creating figure
- apptainer run --app Renv {params.app_path}/pan1c-env.sif Rscript scripts/contig_position.R \
- -b $base/{wildcards.chromosome}.bands \
- -t $base/{wildcards.chromosome}.tsv \
- -o {output.fig}
- """
-
-rule clustering:
- # Read ragtagged fastas and split chromosome sequences into according bins
- input:
- expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
- output:
- expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
- threads: workflow.cores
- params:
- app_path=config["app.path"],
- pan_name=config["name"]
- shell:
- """
- mkdir -p $(dirname {output[0]})
- apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
- --fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
- for file in $(dirname {output[0]})/*.fa; do
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
- done
- """
-
-rule create_allAsm_syri_fig:
- # Create a SyRI figure containing all input assemblies
- input:
- ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
- qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
- output:
- fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
- wrkdir=directory('data/asm.syri/all')
- threads: 8
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir {output.wrkdir}
-
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {input.ref} \
- -q "{input.qry}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- """
-
-rule create_sglAsm_syri_fig:
- # Create a SyRI figure for a single input assembly
- input:
- ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
- qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
- output:
- fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
- wrkdir=directory('data/asm.syri/{haplotype}')
- threads: 4
- retries: 1
- resources:
- mem_gb=48
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir -p {output.wrkdir}
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {input.ref} \
- -q "{input.qry}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- """
\ No newline at end of file
--
GitLab
From bedb03d62a3269ca46ff09bddbddfda40bd40bf3 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 17:05:11 +0200
Subject: [PATCH 38/86] Contact & default wfmash parameters
---
README.md | 3 ++-
config.yaml | 4 ++--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index e2f9df2..04529fb 100644
--- a/README.md
+++ b/README.md
@@ -114,5 +114,6 @@ Pan1c-06AT-v3
This DAG shows the worflow for a pangenome of `Saccharomyces cerevisiae` using the `R64` reference.
-
+# Contact
+[alexis.mergez@inrae.fr](mailto:alexis.mergez@inrae.fr)
diff --git a/config.yaml b/config.yaml
index 3c09fb6..37caa44 100644
--- a/config.yaml
+++ b/config.yaml
@@ -8,8 +8,8 @@ app.path: '<path>'
# Core parameters
# Wfmash alignement parameters :
-wfmash.segment_length: 5000
-wfmash.mapping_id: 90
+wfmash.segment_length: 10000
+wfmash.mapping_id: 95
wfmash.secondary: '-k 19 -H 0.001 -X'
# Seqwish parameters
--
GitLab
From 74593b33bbd6cea30642986d906b2983bbb82b5c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 17:10:17 +0200
Subject: [PATCH 39/86] Changed Odgi viz default parameters
---
config.yaml | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/config.yaml b/config.yaml
index 37caa44..5fe91c1 100644
--- a/config.yaml
+++ b/config.yaml
@@ -16,8 +16,8 @@ wfmash.secondary: '-k 19 -H 0.001 -X'
seqwish.params: '-B 10000000 -k 19 -f 0'
# Odgi 1D and path coverage viz parameters
-odgi.1Dviz.params: '-x 2000 -a 150 -b'
-odgi.pcov.params: '-x 2000 -a 150 -O'
+odgi.1Dviz.params: '-x 2000 -b'
+odgi.pcov.params: '-x 2000 -O'
## Optional parts of the workflow
# Running Quast to get statistics on input haplotypes
--
GitLab
From cf4ca5e948545e498ac3a4f27f10b114489dffcf Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 17:10:32 +0200
Subject: [PATCH 40/86] Added hiddenfile to keep data folder
---
data/.gitkeep | 0
1 file changed, 0 insertions(+), 0 deletions(-)
create mode 100644 data/.gitkeep
diff --git a/data/.gitkeep b/data/.gitkeep
new file mode 100644
index 0000000..e69de29
--
GitLab
From f1ca7b8a10f8b7551db9d7244f375802c0c726e4 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 26 Jun 2024 17:25:13 +0200
Subject: [PATCH 41/86] Moving bgzipping to dedicated rule
---
Snakefile | 4 +++-
rules/tools.smk | 17 ++++++++++++++++-
scripts/ragtagChromInfer.sh | 6 +++---
3 files changed, 22 insertions(+), 5 deletions(-)
diff --git a/Snakefile b/Snakefile
index e3818f2..fc342e4 100644
--- a/Snakefile
+++ b/Snakefile
@@ -73,6 +73,7 @@ def which_analysis():
"""
Rules -------------------------------------------------------------------------------------------
"""
+
# Main target rule
rule all:
input:
@@ -83,6 +84,7 @@ rule all:
"""
Pre-processing section : preparing pggb inputs ---------------------------------------------------
"""
+
rule ragtag_scaffolding:
# Scaffold input haplotype against the reference to infer chromosome scale sequences
input:
@@ -91,7 +93,7 @@ rule ragtag_scaffolding:
refgzi="data/haplotypes/"+config['reference']+".gzi",
fa="data/haplotypes/{haplotype}.fa.gz"
output:
- fa="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz",
+ fa=temp("data/hap.ragtagged/{haplotype}.ragtagged.fa"),
tar="data/hap.ragtagged/{haplotype}.tar.gz"
threads: 8
retries: 1
diff --git a/rules/tools.smk b/rules/tools.smk
index 7528154..5aab858 100644
--- a/rules/tools.smk
+++ b/rules/tools.smk
@@ -13,4 +13,19 @@ rule samtools_index:
app_path=config["app.path"]
shell:
"apptainer run --app samtools {params.app_path}/PanGeTools.sif "
- "faidx {input.fa}"
\ No newline at end of file
+ "faidx {input.fa}"
+
+rule run_bgzip:
+ # Run BGZIP on the file
+ input:
+ "{file}"
+ output:
+ "{file}.gz"
+ threads: 4
+ params:
+ app_path=config["app.path"]
+ shell:
+ """
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads}
+ """
\ No newline at end of file
diff --git a/scripts/ragtagChromInfer.sh b/scripts/ragtagChromInfer.sh
index 9afa538..b8dc8ea 100755
--- a/scripts/ragtagChromInfer.sh
+++ b/scripts/ragtagChromInfer.sh
@@ -41,11 +41,11 @@ grep ">${ref}#chr*" -A1 $tmpdir/ragtag.scaffold.fasta | \
sed "s/${ref}#chr\([^_]*\)_RagTag/${hapID}#chr\1/g" > $tmpdir/${sample}.ragtagged.fa
# Compressing fasta
-apptainer run --app bgzip $appdir/PanGeTools.sif \
- -@ $threads $tmpdir/${sample}.ragtagged.fa
+# apptainer run --app bgzip $appdir/PanGeTools.sif \
+# -@ $threads $tmpdir/${sample}.ragtagged.fa
# Moving fa.gz to output dir
-mv $tmpdir/${sample}.ragtagged.fa.gz $output
+mv $tmpdir/${sample}.ragtagged.fa $output
# Compressing temporary files
tar --remove-files -cf $tmpdir.tar $tmpdir
--
GitLab
From 194a1d59c03af6f5211561118da7c91eb985b1ac Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 10:36:18 +0200
Subject: [PATCH 42/86] Update Snakefile
Offloading chromosome FASTA compression from clustering rule
---
Snakefile | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/Snakefile b/Snakefile
index fc342e4..028e807 100644
--- a/Snakefile
+++ b/Snakefile
@@ -201,8 +201,8 @@ rule clustering:
input:
expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
output:
- expand('data/chrInputs/'+config['name']+'.{chromosome}.fa.gz', chromosome=CHRLIST)
- threads: workflow.cores
+ temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
+ threads: 2
params:
app_path=config["app.path"],
pan_name=config["name"]
@@ -211,9 +211,9 @@ rule clustering:
mkdir -p $(dirname {output[0]})
apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
--fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
- for file in $(dirname {output[0]})/*.fa; do
- apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
- done
+ #for file in $(dirname {output[0]})/*.fa; do
+ # apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
+ #done
"""
rule create_allAsm_syri_fig:
--
GitLab
From 50f491896dfd9066cefdb1230891d1d2c9e9f7a2 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 11:13:21 +0200
Subject: [PATCH 43/86] Update Snakefile
- Removed SyrI rule to get an All assembly figure ( will be replaced with a run of SyRI on chromosomes only instead of all assemblies)
- Renamed some rules for clarity
- Adding more elements to the final report
---
Snakefile | 105 +++++++++++++++++++++++++++++-------------------------
1 file changed, 56 insertions(+), 49 deletions(-)
diff --git a/Snakefile b/Snakefile
index 028e807..b8f2cdb 100644
--- a/Snakefile
+++ b/Snakefile
@@ -196,8 +196,8 @@ rule contig_position:
-o {output.fig}
"""
-rule clustering:
- # Read ragtagged fastas and split chromosome sequences into according bins
+rule chromosome_clustering:
+ # Read ragtagged fastas and split chromosome sequences into according FASTA files
input:
expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
output:
@@ -216,33 +216,9 @@ rule clustering:
#done
"""
-rule create_allAsm_syri_fig:
- # Create a SyRI figure containing all input assemblies
- input:
- ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
- qry=expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
- output:
- fig="output/asm.syri.figs/pan1c."+config['name']+".allAsm.syri.png",
- wrkdir=directory('data/asm.syri/all')
- threads: 8
- params:
- app_path=config["app.path"]
- shell:
- """
- mkdir {output.wrkdir}
-
- bash scripts/getSyriFigs.sh \
- -a {params.app_path} \
- -t {threads} \
- -d {output.wrkdir} \
- -o $(basename {output.fig}) \
- -r {input.ref} \
- -q "{input.qry}"
- mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
- """
-
-rule create_sglAsm_syri_fig:
- # Create a SyRI figure for a single input assembly
+rule SyRI_on_ASM:
+ # Run SyRI on a single assembly.
+ # The assembly is mapped on the 'reference' and SyRI search for SV.
input:
ref="data/hap.ragtagged/"+config['reference'][:-5]+"ragtagged.fa.gz",
qry="data/hap.ragtagged/{haplotype}.ragtagged.fa.gz"
@@ -269,12 +245,11 @@ rule create_sglAsm_syri_fig:
"""
"""
-
Core section : Running PGGB
-
"""
-rule create_pggb_input_syri_fig:
+rule SyRI_on_chrInput:
+ # WIP
input:
fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
output:
@@ -700,43 +675,75 @@ rule create_pan1c_report_fig:
composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
"""
+def get_report_section():
+ """
+ Return 'create_pan1c_report' optional inputs to add them to the final report.
+ For example :
+ - SyRI figures on Assemblies
+ """
+ sections = dict()
+
+ sections["metadata"] = "output/pan1c."+config['name']+".gfa.metadata"
+
+ if config["get_ASMs_SyRI"] == "True":
+ sections["SyRI_on_ASMs_figs"] = expand(
+ "output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
+ haplotype=SAMPLES_NOREF
+ )
+
+ return sections
+
+
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
input:
- figs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
+ odgifigs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv",
+ unpack(get_report_section)
output:
- reportfig="output/pan1c."+config['name']+".report.md"
+ report="output/pan1c."+config['name']+".report.md"
threads: 4
params:
app_path=config['app.path']
run:
- shell("touch {output.reportfig}")
+ shell("touch {output.report}")
+
+ # Adding Summary (made for importing in Joplin)
+ shell("echo '# Summary' >> {output.report}")
+ shell("echo '[TOC]' >> {output.report}")
+ shell("echo '' >> {output.report}")
+
+ # Adding graph construction info
+ ## WIP
- # Adding Summary
- ## To Do
+ # Adding metadata
+ shell("echo '# Graph metadata' >> {output.report}")
+ shell("cat {input.metadata} >> {output.report}")
+ shell("echo '' >> {output.report}")
# Adding General stats
- shell("echo '# General stats' >> {output.reportfig}")
- shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
+ shell("echo '# General stats' >> {output.report}")
+ shell("cat {input.genstats} | csv2md -d $'\\t' >> {output.report}")
+ shell("echo '' >> {output.report}")
# Adding Path stats
- shell("echo '# Path stats' >> {output.reportfig}")
- shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
+ shell("echo '# Path stats' >> {output.report}")
+ shell("cat {input.pathstats} | csv2md -d $'\\t' >> {output.report}")
+ shell("echo '' >> {output.report}")
# Adding chromosomes figures
- fig_list = [fig for fig in input.figs]
+ fig_list = [fig for fig in input.odgifigs]
print(fig_list)
fig_list.sort()
- shell("echo '# Chromosome-scale odgi graphs' >> {output.reportfig}")
+ shell("echo '# Chromosome-scale odgi graphs' >> {output.report}")
for fig in fig_list:
basename=os.path.basename(fig)
chr_name=basename.split('.')[1]
- shell("echo '## {chr_name}' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
- shell("echo '' >> {output.reportfig}")
\ No newline at end of file
+ shell("echo '## {chr_name}' >> {output.report}")
+ shell("echo '' >> {output.report}")
+ shell("echo '' >> {output.report}")
+
+ # Adding SyRI figs if produced
\ No newline at end of file
--
GitLab
From ef1345e67bd8da52e07b0b48ee0e5f46f09b80de Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 11:21:23 +0200
Subject: [PATCH 44/86] Update Snakefile
Added addition of SyRI figs in the final report if wanted
---
Snakefile | 19 +++++++++++++++++--
1 file changed, 17 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index b8f2cdb..fc795e0 100644
--- a/Snakefile
+++ b/Snakefile
@@ -705,7 +705,8 @@ rule create_pan1c_report:
report="output/pan1c."+config['name']+".report.md"
threads: 4
params:
- app_path=config['app.path']
+ app_path=config['app.path'],
+ add_SyRI=config['get_ASMs_SyRI']
run:
shell("touch {output.report}")
@@ -746,4 +747,18 @@ rule create_pan1c_report:
shell("echo '' >> {output.report}")
shell("echo '' >> {output.report}")
- # Adding SyRI figs if produced
\ No newline at end of file
+ # Adding SyRI figs if produced
+ if params.add_SyRI:
+
+ fig_list = [fig for fig in input.SyRI_on_ASMs_figs]
+ fig_list.sort()
+
+ shell("echo '# SyRI on input assemblies' >> {output.report}")
+ for fig in fig_list:
+ basename = os.path.basename(fig)
+ hap_name = basename.split('.')[2:4]
+
+ shell("echo '## {hap_name[0]}, {hap_name[1]}' >> {output.report}")
+ shell("echo '' >> {output.report}")
+
+ shell("echo '' >> {output.report}")
\ No newline at end of file
--
GitLab
From 040bfb9b579aaec0ff9093b4be44fa3d29e6ecc3 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 11:23:45 +0200
Subject: [PATCH 45/86] Update Snakefile
---
Snakefile | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/Snakefile b/Snakefile
index fc795e0..e14cd2d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -675,7 +675,7 @@ rule create_pan1c_report_fig:
composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
"""
-def get_report_section():
+def get_report_sections():
"""
Return 'create_pan1c_report' optional inputs to add them to the final report.
For example :
@@ -684,6 +684,9 @@ def get_report_section():
sections = dict()
sections["metadata"] = "output/pan1c."+config['name']+".gfa.metadata"
+ sections["odgifigs"] = expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST)
+ sections["genstats"] = "output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ sections["pathstats"] = "output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
if config["get_ASMs_SyRI"] == "True":
sections["SyRI_on_ASMs_figs"] = expand(
@@ -697,10 +700,7 @@ def get_report_section():
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
input:
- odgifigs=expand("output/report/"+config['name']+".{chromosome}.report.fig.png", chromosome=CHRLIST),
- genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
- pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv",
- unpack(get_report_section)
+ unpack(get_report_sections)
output:
report="output/pan1c."+config['name']+".report.md"
threads: 4
--
GitLab
From b87480f4c9c5fa6bc8e63ae2fe05fdda5207b25b Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 11:24:25 +0200
Subject: [PATCH 46/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index e14cd2d..5372649 100644
--- a/Snakefile
+++ b/Snakefile
@@ -675,7 +675,7 @@ rule create_pan1c_report_fig:
composite -geometry "+790+$ctgheight" {output.odgifig} {output.reportfig} {output.reportfig}
"""
-def get_report_sections():
+def get_report_sections(wildcards):
"""
Return 'create_pan1c_report' optional inputs to add them to the final report.
For example :
--
GitLab
From 6266a20a58ead08340ffc2cf5e81af09ee12be68 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 27 Jun 2024 16:37:14 +0200
Subject: [PATCH 47/86] Update Snakefile
Added threads to stats jobs
---
Snakefile | 23 ++++++++++-------------
1 file changed, 10 insertions(+), 13 deletions(-)
diff --git a/Snakefile b/Snakefile
index 5372649..1610dd6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -202,7 +202,7 @@ rule chromosome_clustering:
expand('data/hap.ragtagged/{haplotype}.ragtagged.fa.gz', haplotype=SAMPLES)
output:
temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
- threads: 2
+ threads: 1
params:
app_path=config["app.path"],
pan_name=config["name"]
@@ -531,6 +531,7 @@ rule aggregate_graphs_stats:
output:
genstats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv",
pathstats="output/stats/pan1c."+config['name']+".chrGraph.path.stats.tsv"
+ threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
@@ -564,6 +565,7 @@ rule pggb_input_stats:
flag="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
output:
"output/stats/pan1c."+config['name']+".chrInput.stats.tsv"
+ threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
@@ -576,11 +578,12 @@ rule pggb_input_stats:
rule core_statistics:
# Aggregate chrInput, chrGraph and pggb statistics into a single tsv
input:
- chrInputStats="output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
- chrGraphStats="output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
+ chrInputStats = "output/stats/pan1c."+config['name']+".chrInput.stats.tsv",
+ chrGraphStats = "output/stats/pan1c."+config['name']+".chrGraph.general.stats.tsv"
output:
- tsv="output/stats/pan1c."+config['name']+".core.stats.tsv",
- dir=directory("output/pggb.usage.figs")
+ tsv = "output/stats/pan1c."+config['name']+".core.stats.tsv",
+ dir = directory("output/pggb.usage.figs")
+ threads: 1
params:
app_path=config['app.path'],
pan_name=config['name']
@@ -593,12 +596,7 @@ rule core_statistics:
"""
"""
-
-Post-processing section :
- The graph for each chromosome are made as well as some basic statistics.
- In this section, more stats are produced but more specifics ones requiring dedicated tools (Panacus, PAVs for Panache ...).
- It also contains rules to use the graph itself.
-
+Post-processing section
"""
rule get_pav:
# Create PAV matrix readable by panache for a given chromosome scale graph
@@ -694,8 +692,7 @@ def get_report_sections(wildcards):
haplotype=SAMPLES_NOREF
)
- return sections
-
+ return sections
rule create_pan1c_report:
# Produces a markdown report of chromosomes graphs
--
GitLab
From fb1938c8f1b2a79b4f100f5bcba6d4ead6d3b46a Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 3 Jul 2024 09:26:26 +0200
Subject: [PATCH 48/86] Update Snakefile
Added logs to more steps :
- Panacus
- Squeeze
- SyRI
- Quast
- RagTag
---
Snakefile | 51 ++++++++++++++++++++++++++++++++++++++-------------
1 file changed, 38 insertions(+), 13 deletions(-)
diff --git a/Snakefile b/Snakefile
index 1610dd6..7e5773a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -99,15 +99,20 @@ rule ragtag_scaffolding:
retries: 1
params:
app_path=config["app.path"]
+ log:
+ cmd="logs/ragtag/{haplotype}.ragtag.cmd.log",
+ time="logs/ragtag/{haplotype}.ragtag.time.log"
shell:
"""
- bash scripts/ragtagChromInfer.sh \
+ /usr/bin/time -v -o {log.time} \
+ bash scripts/ragtagChromInfer.sh \
-d $(dirname {output.fa})/{wildcards.haplotype} \
-a {params.app_path} \
-t {threads} \
-r {input.ref} \
-q {input.fa} \
- -o {output.fa}
+ -o {output.fa} 2>&1 | \
+ tee {log.cmd}
#if [[ -z $(zgrep '[^[:space:]]' {output.fa}) ]] ; then
# echo "Error : Empty final fasta"
@@ -126,9 +131,13 @@ rule quast_stats:
params:
app_path=config["app.path"],
pan_name=config["name"]
+ log:
+ cmd="logs/quast/{haplotype}.quast.cmd.log",
+ time="logs/quast/{haplotype}.quast.time.log"
shell:
"""
- apptainer run {params.app_path}/pan1c-env.sif quast.py \
+ /usr/bin/time -v -o {log.time} \
+ apptainer run {params.app_path}/pan1c-env.sif quast.py \
-t {threads} \
-o "$(dirname {output.report})" \
-r {input.ref} \
@@ -137,7 +146,8 @@ rule quast_stats:
--no-icarus \
-s \
--large \
- {input.fas}
+ {input.fas} 2>&1 | \
+ tee {log.cmd}
# Compressing temporary files
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
@@ -211,9 +221,6 @@ rule chromosome_clustering:
mkdir -p $(dirname {output[0]})
apptainer run {params.app_path}/pan1c-env.sif python scripts/inputClustering.py \
--fasta {input} --output $(dirname {output[0]}) --panname {params.pan_name}
- #for file in $(dirname {output[0]})/*.fa; do
- # apptainer run --app bgzip {params.app_path}/PanGeTools.sif -@ {threads} $file
- #done
"""
rule SyRI_on_ASM:
@@ -225,6 +232,9 @@ rule SyRI_on_ASM:
output:
fig="output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png",
wrkdir=directory('data/asm.syri/{haplotype}')
+ log:
+ cmd="logs/SyRI_ASM/{haplotype}.SyRI_ASM.cmd.log",
+ time="logs/SyRI_ASM/{haplotype}.SyRI_ASM.time.log"
threads: 4
retries: 1
resources:
@@ -234,13 +244,16 @@ rule SyRI_on_ASM:
shell:
"""
mkdir -p {output.wrkdir}
- bash scripts/getSyriFigs.sh \
+ /usr/bin/time -v -o {log.time} \
+ bash scripts/getSyriFigs.sh \
-a {params.app_path} \
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
-r {input.ref} \
- -q "{input.qry}"
+ -q "{input.qry}" 2>&1 | \
+ tee {log.cmd}
+
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
"""
@@ -470,15 +483,22 @@ rule graph_squeeze:
graphs=expand('data/chrGraphs/'+config['name']+'.{chromosome}.gfa', chromosome=CHRLIST)
output:
"output/pan1c."+config['name']+".gfa"
+ log:
+ cmd="logs/squeeze/"+config['name']+".squeeze.cmd.log",
+ time="logs/squeeze/"+config['name']+".squeeze.time.log",
threads: 16
params:
app_path=config['app.path']
shell:
"""
- apptainer run --app odgi {params.app_path}/PanGeTools.sif \
- squeeze -t {threads} -O -P -f {input.glist} -o {output}.og
+ /usr/bin/time -v -o {log.time} \
+ apptainer run --app odgi {params.app_path}/PanGeTools.sif \
+ squeeze -t {threads} -O -P -f {input.glist} -o {output}.og 2>&1 | \
+ tee {log.cmd}
+
apptainer run --app odgi {params.app_path}/PanGeTools.sif \
view -t {threads} -P -i {output}.og -g > {output}
+
rm {output}.og
"""
@@ -622,6 +642,9 @@ rule panacus_stats:
graph='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
output:
html='output/panacus.reports/'+config['name']+'.{chromosome}.histgrowth.html'
+ log:
+ cmd="logs/panacus/{chromosome}.panacus.cmd.log",
+ time="logs/panacus/{chromosome}.panacus.time.log"
params:
app_path=config['app.path'],
pan_name=config['name'],
@@ -629,13 +652,15 @@ rule panacus_stats:
threads: 8
shell:
"""
- bash scripts/getPanacusHG.sh \
+ /usr/bin/time -v -o {log.time} \
+ bash scripts/getPanacusHG.sh \
-g {input.graph} \
-r $(basename {params.refname} .fa.gz) \
-d data/chrGraphs/{wildcards.chromosome} \
-o {output.html} \
-a {params.app_path} \
- -t {threads}
+ -t {threads} 2>&1 | \
+ tee {log.cmd}
"""
rule create_pan1c_report_fig:
--
GitLab
From c6c377917d516431653b6d489b00826a51f04630 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Wed, 3 Jul 2024 09:28:29 +0200
Subject: [PATCH 49/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 7e5773a..5839de7 100644
--- a/Snakefile
+++ b/Snakefile
@@ -132,8 +132,8 @@ rule quast_stats:
app_path=config["app.path"],
pan_name=config["name"]
log:
- cmd="logs/quast/{haplotype}.quast.cmd.log",
- time="logs/quast/{haplotype}.quast.time.log"
+ cmd="logs/quast/quast.cmd.log",
+ time="logs/quast/quast.time.log"
shell:
"""
/usr/bin/time -v -o {log.time} \
--
GitLab
From 61f7281cf117f239d2af017a223011a68e599285 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 4 Jul 2024 09:10:09 +0200
Subject: [PATCH 50/86] Update tools.smk
---
rules/tools.smk | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/rules/tools.smk b/rules/tools.smk
index 5aab858..53fe1ff 100644
--- a/rules/tools.smk
+++ b/rules/tools.smk
@@ -27,5 +27,5 @@ rule run_bgzip:
shell:
"""
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
- -@ {threads}
+ -@ {threads} {input}
"""
\ No newline at end of file
--
GitLab
From 2ca1fc4e14a6e75a4f671ffe5b1cd4fed4a3f518 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 4 Jul 2024 15:30:37 +0200
Subject: [PATCH 51/86] Update Snakefile
---
Snakefile | 2 ++
1 file changed, 2 insertions(+)
diff --git a/Snakefile b/Snakefile
index 5839de7..1abfc61 100644
--- a/Snakefile
+++ b/Snakefile
@@ -742,7 +742,9 @@ rule create_pan1c_report:
# Adding metadata
shell("echo '# Graph metadata' >> {output.report}")
+ shell("echo '```' >> {output.report}")
shell("cat {input.metadata} >> {output.report}")
+ shell("echo '```' >> {output.report}")
shell("echo '' >> {output.report}")
# Adding General stats
--
GitLab
From a7593a90e16c94afdf7baf21526441fde10f100e Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:14:29 +0200
Subject: [PATCH 52/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 1abfc61..ac6421f 100644
--- a/Snakefile
+++ b/Snakefile
@@ -279,7 +279,7 @@ rule SyRI_on_chrInput:
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
- '/^>/ {OUT="{output.wrkdir}" substr($0,2) ".fa"}; {print >> OUT; close(OUT)}'
+ '/^>/ {{OUT="{output.wrkdir}" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
## Getting the list of sequences
asmList=()
--
GitLab
From 33802127ef3fed52872ba2709c92dfdad977b891 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:16:07 +0200
Subject: [PATCH 53/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index ac6421f..793aef4 100644
--- a/Snakefile
+++ b/Snakefile
@@ -294,7 +294,7 @@ rule SyRI_on_chrInput:
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
- -r {output.wrkdir}/"${refname}.fa" \
+ -r {output.wrkdir}/"${{refname}}.fa" \
-q "${asmList[@]}"
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
--
GitLab
From 2e8e05af134a7d7e231257267a7f65aaaa929ba1 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:16:51 +0200
Subject: [PATCH 54/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 793aef4..499b8dd 100644
--- a/Snakefile
+++ b/Snakefile
@@ -295,7 +295,7 @@ rule SyRI_on_chrInput:
-d {output.wrkdir} \
-o $(basename {output.fig}) \
-r {output.wrkdir}/"${{refname}}.fa" \
- -q "${asmList[@]}"
+ -q "${{asmList[@]}}"
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
"""
--
GitLab
From 02dcafaeed179468e840d1d6878c67c1decd7704 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:18:48 +0200
Subject: [PATCH 55/86] Update Snakefile
---
Snakefile | 2 ++
1 file changed, 2 insertions(+)
diff --git a/Snakefile b/Snakefile
index 499b8dd..2b49ce5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -280,6 +280,8 @@ rule SyRI_on_chrInput:
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
'/^>/ {{OUT="{output.wrkdir}" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
+
+ grep '>' {output.wrkdir}/*.fa
## Getting the list of sequences
asmList=()
--
GitLab
From 13721c88cdee86ad13bf4d83537897387bd7a059 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:21:06 +0200
Subject: [PATCH 56/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 2b49ce5..26a0210 100644
--- a/Snakefile
+++ b/Snakefile
@@ -267,7 +267,7 @@ rule SyRI_on_chrInput:
fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
output:
fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
- wrkdir=directory('data/chrInput/syri/{chromosome}')
+ wrkdir=directory('data/chrInputs/syri/{chromosome}/')
threads: 8
params:
app_path=config["app.path"],
--
GitLab
From f3a90a07bb9f4676d882cf79efefb7fbfd2ef28b Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:23:50 +0200
Subject: [PATCH 57/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 26a0210..9460fbf 100644
--- a/Snakefile
+++ b/Snakefile
@@ -267,7 +267,7 @@ rule SyRI_on_chrInput:
fasta='data/chrInputs/'+config['name']+'.{chromosome}.fa.gz'
output:
fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
- wrkdir=directory('data/chrInputs/syri/{chromosome}/')
+ wrkdir=directory('data/chrInputs/syri/{chromosome}')
threads: 8
params:
app_path=config["app.path"],
@@ -279,7 +279,7 @@ rule SyRI_on_chrInput:
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
- '/^>/ {{OUT="{output.wrkdir}" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
+ '/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
grep '>' {output.wrkdir}/*.fa
--
GitLab
From be9cbe44ae911968e43e54fa8ab4755342c73977 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:28:34 +0200
Subject: [PATCH 58/86] Update Snakefile
---
Snakefile | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 9460fbf..84f47f6 100644
--- a/Snakefile
+++ b/Snakefile
@@ -268,7 +268,7 @@ rule SyRI_on_chrInput:
output:
fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
wrkdir=directory('data/chrInputs/syri/{chromosome}')
- threads: 8
+ threads: workflow.cores
params:
app_path=config["app.path"],
ref=config['reference']
@@ -282,6 +282,8 @@ rule SyRI_on_chrInput:
'/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
grep '>' {output.wrkdir}/*.fa
+ apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
+ -@ {threads} {output.wrkdir}/*.fa
## Getting the list of sequences
asmList=()
--
GitLab
From 7ce85183a84af0db35d88c1d054d74ffd2353241 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:29:46 +0200
Subject: [PATCH 59/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index 84f47f6..0820f13 100644
--- a/Snakefile
+++ b/Snakefile
@@ -287,8 +287,8 @@ rule SyRI_on_chrInput:
## Getting the list of sequences
asmList=()
- for file in {output.wrkdir}/*.fa; do
- asm="$(basename $file .fa | cut -f1 -d"#").fa"
+ for file in {output.wrkdir}/*.fa.gz; do
+ asm="$(basename $file .fa.gz | cut -f1 -d"#").fa.gz"
mv $file "$(dirname $file)/$asm"
asmList+=("$asm")
done
--
GitLab
From a02ff604b899b089858b0d0db5241fb836405f45 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:30:59 +0200
Subject: [PATCH 60/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 0820f13..c6dea3b 100644
--- a/Snakefile
+++ b/Snakefile
@@ -298,7 +298,7 @@ rule SyRI_on_chrInput:
-t {threads} \
-d {output.wrkdir} \
-o $(basename {output.fig}) \
- -r {output.wrkdir}/"${{refname}}.fa" \
+ -r {output.wrkdir}/"${{refname}}.fa.gz" \
-q "${{asmList[@]}}"
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
--
GitLab
From 16a9997590055486ddf2fdae9cf4c93ec6c69748 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:32:25 +0200
Subject: [PATCH 61/86] Update Snakefile
---
Snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index c6dea3b..eafe179 100644
--- a/Snakefile
+++ b/Snakefile
@@ -281,10 +281,10 @@ rule SyRI_on_chrInput:
zcat {input.fasta} | awk -F"#" \
'/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
- grep '>' {output.wrkdir}/*.fa
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} {output.wrkdir}/*.fa
-
+ zgrep '>' {output.wrkdir}/*.fa
+
## Getting the list of sequences
asmList=()
for file in {output.wrkdir}/*.fa.gz; do
--
GitLab
From 701dd233cc9e506944941ae965bc755d8639aab3 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:33:48 +0200
Subject: [PATCH 62/86] Update Snakefile
---
Snakefile | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index eafe179..e3977c5 100644
--- a/Snakefile
+++ b/Snakefile
@@ -281,9 +281,10 @@ rule SyRI_on_chrInput:
zcat {input.fasta} | awk -F"#" \
'/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
+ ls
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} {output.wrkdir}/*.fa
- zgrep '>' {output.wrkdir}/*.fa
+ zgrep '>' {output.wrkdir}/*.fa.gz
## Getting the list of sequences
asmList=()
--
GitLab
From 4e32c41d2e119d15819408954b17bdca064e4cdf Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:37:29 +0200
Subject: [PATCH 63/86] Update Snakefile
---
Snakefile | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/Snakefile b/Snakefile
index e3977c5..f3d98c9 100644
--- a/Snakefile
+++ b/Snakefile
@@ -281,7 +281,6 @@ rule SyRI_on_chrInput:
zcat {input.fasta} | awk -F"#" \
'/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
- ls
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} {output.wrkdir}/*.fa
zgrep '>' {output.wrkdir}/*.fa.gz
@@ -291,7 +290,7 @@ rule SyRI_on_chrInput:
for file in {output.wrkdir}/*.fa.gz; do
asm="$(basename $file .fa.gz | cut -f1 -d"#").fa.gz"
mv $file "$(dirname $file)/$asm"
- asmList+=("$asm")
+ asmList+=("$(dirname $file)/$asm")
done
bash scripts/getSyriFigs.sh \
--
GitLab
From 4892e9bc9d170ddd8ebfbb159903ec5d5add4eab Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 11:53:38 +0200
Subject: [PATCH 64/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 3baf716..dc4b0f8 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -36,6 +36,8 @@ for item in "${temp[@]}"; do
fi
done
+echo "${asmList[@]}"
+
# Array to store the created syri files
syriFileList=()
@@ -45,8 +47,8 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Setting filepaths for later
bamFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).bam"
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
- #hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
- #refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
# Debug
echo -e "[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID"
--
GitLab
From 6a09682cf95f923893caef5a4fad3cc2cd034dc7 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:28:42 +0200
Subject: [PATCH 65/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index dc4b0f8..5e1ed5a 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -36,7 +36,7 @@ for item in "${temp[@]}"; do
fi
done
-echo "${asmList[@]}"
+echo -e "${asmList[@]}"
# Array to store the created syri files
syriFileList=()
--
GitLab
From a263bd73bbada19908622df4c4cabed1c1adb87f Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:33:19 +0200
Subject: [PATCH 66/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 5e1ed5a..724c1fd 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -36,7 +36,7 @@ for item in "${temp[@]}"; do
fi
done
-echo -e "${asmList[@]}"
+echo "The array : ${asmList[@]}"
# Array to store the created syri files
syriFileList=()
--
GitLab
From bbe34e4ed6eb8e7c7c4aaab324ce126b336425d4 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:36:58 +0200
Subject: [PATCH 67/86] Update Snakefile
---
Snakefile | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index f3d98c9..188937d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -286,12 +286,14 @@ rule SyRI_on_chrInput:
zgrep '>' {output.wrkdir}/*.fa.gz
## Getting the list of sequences
- asmList=()
+ AllAsmList=()
for file in {output.wrkdir}/*.fa.gz; do
asm="$(basename $file .fa.gz | cut -f1 -d"#").fa.gz"
mv $file "$(dirname $file)/$asm"
- asmList+=("$(dirname $file)/$asm")
+ AllAsmList+=("$(dirname $file)/$asm")
done
+
+ echo "The ASM Array : ${{AllAsmList[@]}}"
bash scripts/getSyriFigs.sh \
-a {params.app_path} \
@@ -299,7 +301,7 @@ rule SyRI_on_chrInput:
-d {output.wrkdir} \
-o $(basename {output.fig}) \
-r {output.wrkdir}/"${{refname}}.fa.gz" \
- -q "${{asmList[@]}}"
+ -q "${{AllAsmList[@]}}"
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
"""
--
GitLab
From 02d0e4b733af1958ab221caab1effab9f4b6f2ae Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:44:59 +0200
Subject: [PATCH 68/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 3 +++
1 file changed, 3 insertions(+)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 724c1fd..dc70828 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -28,7 +28,10 @@ done
# Reading query argument and creating an array containing the path to query fasta files
IFS=' ' read -r -a temp <<< "$qry"
+echo "tempArr : ${temp[@]}"
+
asmList=("$ref")
+
# Sorting the array to put the reference in first
for item in "${temp[@]}"; do
if [[ $item != "$ref" ]]; then
--
GitLab
From 0b15696608296670320bf294490400581d54a41c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:46:52 +0200
Subject: [PATCH 69/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 1 +
1 file changed, 1 insertion(+)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index dc70828..fe81ce8 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -28,6 +28,7 @@ done
# Reading query argument and creating an array containing the path to query fasta files
IFS=' ' read -r -a temp <<< "$qry"
+echo "Query : $qry"
echo "tempArr : ${temp[@]}"
asmList=("$ref")
--
GitLab
From bb6529350be5e348fbdd3a8342c795582c6f6fd2 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 13:55:22 +0200
Subject: [PATCH 70/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 188937d..ee9cc90 100644
--- a/Snakefile
+++ b/Snakefile
@@ -301,7 +301,7 @@ rule SyRI_on_chrInput:
-d {output.wrkdir} \
-o $(basename {output.fig}) \
-r {output.wrkdir}/"${{refname}}.fa.gz" \
- -q "${{AllAsmList[@]}}"
+ -q "${{AllAsmList[*]}}"
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
"""
--
GitLab
From 119d8e1d880e6fac876738e2cabe8aee8e304b09 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 14:09:09 +0200
Subject: [PATCH 71/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index ee9cc90..e3491b4 100644
--- a/Snakefile
+++ b/Snakefile
@@ -279,7 +279,7 @@ rule SyRI_on_chrInput:
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
- '/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
+ '/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".hap" substr($0,3) ".fa"}}; {{print >> OUT; close(OUT)}}'
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} {output.wrkdir}/*.fa
--
GitLab
From 67e49a0c1e995e74646658f824d173d96be0b133 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 14:19:04 +0200
Subject: [PATCH 72/86] Update Snakefile
---
Snakefile | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/Snakefile b/Snakefile
index e3491b4..46ff6a2 100644
--- a/Snakefile
+++ b/Snakefile
@@ -279,16 +279,16 @@ rule SyRI_on_chrInput:
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
- '/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".hap" substr($0,3) ".fa"}}; {{print >> OUT; close(OUT)}}'
+ '/^>/ {{OUT="{output.wrkdir}/" substr($0,2) ".fa"}}; {{print >> OUT; close(OUT)}}'
apptainer run --app bgzip {params.app_path}/PanGeTools.sif \
-@ {threads} {output.wrkdir}/*.fa
- zgrep '>' {output.wrkdir}/*.fa.gz
+ #zgrep '>' {output.wrkdir}/*.fa.gz
## Getting the list of sequences
AllAsmList=()
for file in {output.wrkdir}/*.fa.gz; do
- asm="$(basename $file .fa.gz | cut -f1 -d"#").fa.gz"
+ asm="$(basename $file .fa.gz | cut -f1,2 -d"#" | sed 's/#/\.hap/').fa.gz"
mv $file "$(dirname $file)/$asm"
AllAsmList+=("$(dirname $file)/$asm")
done
--
GitLab
From b3cac8129237d833412e9b3e1c88b0e85c9f19cf Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 14:19:53 +0200
Subject: [PATCH 73/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 46ff6a2..68c535d 100644
--- a/Snakefile
+++ b/Snakefile
@@ -288,7 +288,7 @@ rule SyRI_on_chrInput:
## Getting the list of sequences
AllAsmList=()
for file in {output.wrkdir}/*.fa.gz; do
- asm="$(basename $file .fa.gz | cut -f1,2 -d"#" | sed 's/#/\.hap/').fa.gz"
+ asm="$(basename $file .fa.gz | cut -f1,2 -d"#" | sed 's/#/\\.hap/').fa.gz"
mv $file "$(dirname $file)/$asm"
AllAsmList+=("$(dirname $file)/$asm")
done
--
GitLab
From 93238a63287d70f5338bbaa97d5c16142d3cb743 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 14:29:21 +0200
Subject: [PATCH 74/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 68c535d..c03ec33 100644
--- a/Snakefile
+++ b/Snakefile
@@ -275,7 +275,7 @@ rule SyRI_on_chrInput:
shell:
"""
mkdir {output.wrkdir}
- refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1)
+ refname=$(basename {params.ref} .fa.gz | cut -d'.' -f1,2)
## Creating single fasta from multifasta
zcat {input.fasta} | awk -F"#" \
--
GitLab
From 1ac7f9875caf20319afc040f1509c15de53b4439 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 14:42:54 +0200
Subject: [PATCH 75/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index fe81ce8..51ccfa5 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -27,20 +27,21 @@ done
## Main script
# Reading query argument and creating an array containing the path to query fasta files
IFS=' ' read -r -a temp <<< "$qry"
+readarray -td '' temp_sorted < <(printf '%s\0' "${temp[@]}" | sort -z)
-echo "Query : $qry"
-echo "tempArr : ${temp[@]}"
+#echo "Query : $qry"
+#echo "tempArr : ${temp[@]}"
asmList=("$ref")
# Sorting the array to put the reference in first
-for item in "${temp[@]}"; do
+for item in "${temp_sorted[@]}"; do
if [[ $item != "$ref" ]]; then
asmList+=($item)
fi
done
-echo "The array : ${asmList[@]}"
+#echo "The array : ${asmList[@]}"
# Array to store the created syri files
syriFileList=()
@@ -51,11 +52,11 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Setting filepaths for later
bamFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).bam"
syriFile="$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz).syri.out"
- hapID=$(basename ${asmList[i + 1]} .ragtagged.fa.gz | sed 's/.hap/#/')
- refID=$(basename ${asmList[i]} .ragtagged.fa.gz | sed 's/.hap/#/')
+ hapID=$(basename ${asmList[i + 1]})
+ refID=$(basename ${asmList[i]})
# Debug
- echo -e "[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID"
+ echo -e "\n[Debug::SyRI_script::$hapID] hapID: $hapID\trefID: $refID\n"
# Adding the output syri file to the array
syriFileList+=($syriFile)
--
GitLab
From 13b49a01a058ac488f5e309a3f51deba49b9ae14 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Fri, 5 Jul 2024 18:05:13 +0200
Subject: [PATCH 76/86] Updated SyRI script
Added width and height to SyRI script
---
Snakefile | 3 ++-
scripts/getSyriFigs.sh | 10 +++++++---
2 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index c03ec33..e38f585 100644
--- a/Snakefile
+++ b/Snakefile
@@ -301,7 +301,8 @@ rule SyRI_on_chrInput:
-d {output.wrkdir} \
-o $(basename {output.fig}) \
-r {output.wrkdir}/"${{refname}}.fa.gz" \
- -q "${{AllAsmList[*]}}"
+ -q "${{AllAsmList[*]}}" \
+ -h 9 -w 16
mv {output.wrkdir}/$(basename {output.fig}) {output.fig}
rm {output.wrkdir}/*.fa
"""
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 51ccfa5..848e2e4 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -9,9 +9,11 @@ appdir="" # Directory containing apptainer images
threads=""
wrkdir="" # Working directory (directory used by pggb to store step files like .paf, etc...)
output="" # Output Syri figure(s)
+height=16 # Figure height
+width=9 # Figure width
## Getting arguments
-while getopts "r:q:a:t:d:o:" option; do
+while getopts "r:q:a:t:d:o:h:w:" option; do
case "$option" in
r) ref="$OPTARG";;
q) qry="$OPTARG";;
@@ -19,7 +21,9 @@ while getopts "r:q:a:t:d:o:" option; do
t) threads="$OPTARG";;
d) wrkdir="$OPTARG";;
o) output="$OPTARG";;
- \?) echo "Usage: $0 [-r ref] [-q query] [-a appdir] [-t threads] [-d wrkdir] [-o output]" >&2
+ h) height="$OPTARG";;
+ w) width="$OPTARG";;
+ \?) echo "Usage: $0 [-r ref] [-q query] [-a appdir] [-t threads] [-d wrkdir] [-o output] [-h height] [-w width]" >&2
exit 1;;
esac
done
@@ -93,7 +97,7 @@ for asm in "${asmList[@]}"; do
done
# Generating the plotsr command
-command="--genomes $wrkdir/genomes.txt -o $wrkdir/$output -f 12 -H 16 -W 9 -d 600 "
+command="--genomes $wrkdir/genomes.txt -o $wrkdir/$output -f 12 -H $height -W $width -d 600 "
# Adding syri files to the command as each needs to be specified using "--sr" argument
for file in "${syriFileList[@]}"; do
--
GitLab
From b59f1f312c49d5fa0af2fc035ef1b564d9a10589 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 8 Jul 2024 11:01:14 +0200
Subject: [PATCH 77/86] Added Syri on chrInputs
---
Snakefile | 9 +++++++--
config.yaml | 2 +-
example/config_CICD.yaml | 3 ++-
3 files changed, 10 insertions(+), 4 deletions(-)
diff --git a/Snakefile b/Snakefile
index e38f585..c493eea 100644
--- a/Snakefile
+++ b/Snakefile
@@ -50,9 +50,13 @@ def which_analysis():
if config["get_PAV"] == "True": # Adding PAV matrix creation
analysis_inputs.append("output/pav.matrices")
- if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each figures
+ if config["get_ASMs_SyRI"] == "True": # Creating SyRI for each input assembly
analysis_inputs.append(
- expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF),
+ expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF)
+ )
+ if config["get_chrInputs_SyRI"] == "True": # Creating SyRI figures for each PGGB input
+ analysis_input.append(
+ expand("output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png", chromosome=CHRLIST)
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
analysis_inputs.append(
@@ -576,6 +580,7 @@ rule final_graph_tagging:
output:
"output/pan1c."+config['name']+".gfa.metadata"
threads: 1
+ priority: 100
params:
app_path=config['app.path'],
pan_name=config['name']
diff --git a/config.yaml b/config.yaml
index 5fe91c1..0a8502a 100644
--- a/config.yaml
+++ b/config.yaml
@@ -27,7 +27,7 @@ get_contig_pos: 'True'
# Computes Presence Absence Variant matrices for Panache (not recommended; very long)
get_PAV: 'False'
# Computes SyRI figures for haplotypes
-#get_allASM_SyRI: 'False' # All vs all
get_ASMs_SyRI: 'False' # Haplotype vs Reference
+get_chrInputs_SyRI: 'False' # SyRI on chrInputs
# Creating final report
create_report: 'True'
diff --git a/example/config_CICD.yaml b/example/config_CICD.yaml
index 648e686..cc0c279 100644
--- a/example/config_CICD.yaml
+++ b/example/config_CICD.yaml
@@ -28,6 +28,7 @@ get_contig_pos: 'True'
get_PAV: 'False'
# Computes SyRI figures for haplotypes
#get_allASM_SyRI: 'False' # All vs all
-get_ASMs_SyRI: 'False' # Haplotype vs Reference
+get_ASMs_SyRI: 'True' # Haplotype vs Reference
+get_chrInputs_SyRI: 'True' # SyRI on chrInputs
# Creating final report
create_report: 'True'
--
GitLab
From b4779c67f09da8ce25b0996a60aeadd37e33fe71 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Mon, 8 Jul 2024 11:06:41 +0200
Subject: [PATCH 78/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index c493eea..7420323 100644
--- a/Snakefile
+++ b/Snakefile
@@ -55,7 +55,7 @@ def which_analysis():
expand("output/asm.syri.figs/pan1c."+config['name']+".{haplotype}.syri.png", haplotype=SAMPLES_NOREF)
)
if config["get_chrInputs_SyRI"] == "True": # Creating SyRI figures for each PGGB input
- analysis_input.append(
+ analysis_inputs.append(
expand("output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png", chromosome=CHRLIST)
)
if config["run_Quast"] == "True": # Running Quast on input haplotypes
--
GitLab
From 867217fd644f7c180e3187f4754d34b3a87c426c Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 10:40:14 +0200
Subject: [PATCH 79/86] Update Snakefile
---
Snakefile | 8 ++++++++
1 file changed, 8 insertions(+)
diff --git a/Snakefile b/Snakefile
index e38f585..a5d3272 100644
--- a/Snakefile
+++ b/Snakefile
@@ -97,6 +97,7 @@ rule ragtag_scaffolding:
tar="data/hap.ragtagged/{haplotype}.tar.gz"
threads: 8
retries: 1
+ priority: 100
params:
app_path=config["app.path"]
log:
@@ -213,6 +214,7 @@ rule chromosome_clustering:
output:
temp(expand('data/chrInputs/'+config['name']+'.{chromosome}.fa', chromosome=CHRLIST))
threads: 1
+ priority: 100
params:
app_path=config["app.path"],
pan_name=config["name"]
@@ -316,6 +318,7 @@ rule wfmash_on_chr:
mapping=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.mapping.paf"),
aln=temp("data/chrGraphs/{chromosome}/{chromosome}.wfmash.aln.paf")
threads: 16
+ priority: 100
params:
app_path=config['app.path'],
segment_length=config['wfmash.segment_length'],
@@ -365,6 +368,7 @@ rule seqwish:
output:
temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfa")
threads: 8
+ priority: 100
params:
app_path=config['app.path'],
seqwish=config['seqwish.params']
@@ -393,6 +397,7 @@ rule gfaffix_on_chr:
gfa=temp("data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.gfa"),
transform="data/chrGraphs/{chromosome}/{chromosome}.seqwish.gfaffixD.transform.txt"
threads: 1
+ priority: 100
params:
app_path=config['app.path']
log:
@@ -416,6 +421,7 @@ rule odgi_postprocessing:
output:
gfa='data/chrGraphs/'+config['name']+'.{chromosome}.gfa'
threads: 8
+ priority: 100
params:
app_path=config['app.path']
log:
@@ -478,6 +484,7 @@ rule generate_graph_list:
output:
"data/chrGraphs/graphsList.txt"
threads: 1
+ priority: 100
run:
with open(output[0], "w") as handle:
for file in input:
@@ -494,6 +501,7 @@ rule graph_squeeze:
cmd="logs/squeeze/"+config['name']+".squeeze.cmd.log",
time="logs/squeeze/"+config['name']+".squeeze.time.log",
threads: 16
+ priority: 100
params:
app_path=config['app.path']
shell:
--
GitLab
From 1ccf65891b89b9b983c4fc30d016e94d302a9242 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 10:55:17 +0200
Subject: [PATCH 80/86] Update syri_pruning.py
Unifying chromosome sequence record's name to prevent SyRI from erroring out when input chromosomes can be matched with 2 query chromosomes
---
scripts/syri_pruning.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/scripts/syri_pruning.py b/scripts/syri_pruning.py
index 811e2b9..2482cb2 100644
--- a/scripts/syri_pruning.py
+++ b/scripts/syri_pruning.py
@@ -62,6 +62,7 @@ with gzip.open(args.ref, 'rt') as handle:
chrname = record.id.split("#")[-1]
chrList.append(chrname)
seqDict[name][chrname] = record
+ seqDict[name][chrname].id = chrname
# Parsing fasta files
for filename in args.fastafiles:
@@ -74,6 +75,7 @@ for filename in args.fastafiles:
for record in sequences:
chrname = record.id.split("#")[-1]
seqDict[name][chrname] = record
+ seqDict[name][chrname].id = chrname
# Getting the list of common chromosomes
for hap, chromosomes in seqDict.items():
--
GitLab
From ea67debd266fb5851d34c29973443d7f04b71e43 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 12:15:38 +0200
Subject: [PATCH 81/86] Update getSyriFigs.sh
Using prunned FASTAs instead of input FASTAs
---
scripts/getSyriFigs.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 848e2e4..07cdec7 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -84,7 +84,7 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Syri on previous alignment
apptainer run $appdir/pan1c-env.sif \
- syri -c $wrkdir/$bamFile -r ${asmList[i]} -q ${asmList[i + 1]} -k -F B \
+ syri -c $wrkdir/$bamFile -r $wrkdir/$(basename ${asmList[i]} .gz) -q $wrkdir/$(basename ${asmList[i + 1]} .gz) -k -F B \
--nc $threads \
--dir $wrkdir --prefix "$(basename ${asmList[i]} .fa.gz)_$(basename ${asmList[i + 1]} .fa.gz)."
done
--
GitLab
From 204d3b62b6932029f4664554fbee0a7dfc59984a Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 15:53:30 +0200
Subject: [PATCH 82/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 07cdec7..92b1cdb 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -69,6 +69,11 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
apptainer run $appdir/pan1c-env.sif python scripts/syri_pruning.py \
-r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir
+ echo "\n[Debug::SyRI_script::$hapID] REF"
+ grep '>' ${asmList[i]}
+ echo "\n[Debug::SyRI_script::$hapID] QRY"
+ grep '>' ${asmList[i + 1]}
+
# Renaming chromosomes with same ids as the reference (Not working)
#sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
--
GitLab
From ba890499fe98c030df6542da90dbe262994796de Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 15:55:57 +0200
Subject: [PATCH 83/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 92b1cdb..972d2dc 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -70,10 +70,10 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
-r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir
echo "\n[Debug::SyRI_script::$hapID] REF"
- grep '>' ${asmList[i]}
+ grep '>' $wrkdir/$(basename ${asmList[i]} .gz)
echo "\n[Debug::SyRI_script::$hapID] QRY"
- grep '>' ${asmList[i + 1]}
-
+ grep '>' $wrkdir/$(basename ${asmList[i + 1]} .gz)
+
# Renaming chromosomes with same ids as the reference (Not working)
#sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
--
GitLab
From 2cad655b30c1917c30bdda9000eaf6cabb9ea1b1 Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 15:57:56 +0200
Subject: [PATCH 84/86] Update getSyriFigs.sh
---
scripts/getSyriFigs.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index 972d2dc..e85ea25 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -98,7 +98,7 @@ done
# Each line contains 2 columns : fasta filepath and its simpler name
echo -e "#files\tname" > $wrkdir/genomes.txt
for asm in "${asmList[@]}"; do
- echo -e "${asm}\t$(basename $asm .fa.gz | cut -d'.' -f1)" >> $wrkdir/genomes.txt
+ echo -e "$wrkdir/$(basename ${asm} .gz)\t$(basename $asm .fa.gz | cut -d'.' -f1)" >> $wrkdir/genomes.txt
done
# Generating the plotsr command
--
GitLab
From 059b5f346bece0dcfc40bca951de04c7711d14bb Mon Sep 17 00:00:00 2001
From: Alexis Mergez <alexis.mergez@inrae.fr>
Date: Tue, 9 Jul 2024 16:06:07 +0200
Subject: [PATCH 85/86] Update Snakefile
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 94cb1f6..a86dcef 100644
--- a/Snakefile
+++ b/Snakefile
@@ -274,7 +274,7 @@ rule SyRI_on_chrInput:
output:
fig="output/chrInput.syri.figs/"+config['name']+".{chromosome}.asm.syri.png",
wrkdir=directory('data/chrInputs/syri/{chromosome}')
- threads: workflow.cores
+ threads: 8
params:
app_path=config["app.path"],
ref=config['reference']
--
GitLab
From 249b23d0fd2492d4d43581c8d9b7a00d986249fc Mon Sep 17 00:00:00 2001
From: Alexis Mergez <amergez@miat-pret-5.toulouse.inrae.fr>
Date: Thu, 11 Jul 2024 12:15:39 +0200
Subject: [PATCH 86/86] Silented some debug lines
---
Snakefile | 2 +-
scripts/getSyriFigs.sh | 10 +++++-----
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/Snakefile b/Snakefile
index a86dcef..71c2bb3 100644
--- a/Snakefile
+++ b/Snakefile
@@ -299,7 +299,7 @@ rule SyRI_on_chrInput:
AllAsmList+=("$(dirname $file)/$asm")
done
- echo "The ASM Array : ${{AllAsmList[@]}}"
+ #echo "The ASM Array : ${{AllAsmList[@]}}"
bash scripts/getSyriFigs.sh \
-a {params.app_path} \
diff --git a/scripts/getSyriFigs.sh b/scripts/getSyriFigs.sh
index e85ea25..84f93c2 100755
--- a/scripts/getSyriFigs.sh
+++ b/scripts/getSyriFigs.sh
@@ -67,12 +67,12 @@ for ((i = 0; i < ${#asmList[@]} - 1; i++)); do
# Prunning fasta files based of common chromosomes
apptainer run $appdir/pan1c-env.sif python scripts/syri_pruning.py \
- -r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir
+ -r ${asmList[i]} -f ${asmList[i + 1]} -o $wrkdir -d
- echo "\n[Debug::SyRI_script::$hapID] REF"
- grep '>' $wrkdir/$(basename ${asmList[i]} .gz)
- echo "\n[Debug::SyRI_script::$hapID] QRY"
- grep '>' $wrkdir/$(basename ${asmList[i + 1]} .gz)
+ #echo "\n[Debug::SyRI_script::$hapID] REF"
+ #grep '>' $wrkdir/$(basename ${asmList[i]} .gz)
+ #echo "\n[Debug::SyRI_script::$hapID] QRY"
+ #grep '>' $wrkdir/$(basename ${asmList[i + 1]} .gz)
# Renaming chromosomes with same ids as the reference (Not working)
#sed -i "s/${hapID}#chr/${refID}#chr/g" $wrkdir/$(basename ${asmList[i + 1]} .gz)
--
GitLab