From 9d905ba193c30bf57a526afd2292f2a05e617c8d Mon Sep 17 00:00:00 2001
From: mariabernard <maria.bernard@jouy.inra.fr>
Date: Thu, 14 Mar 2019 15:47:11 +0100
Subject: [PATCH] change bgzip\tabix management and temp files definition
---
.../rules/combine_genotypeGVCF.rules | 5 +++-
Snakemake/IMAGE_calling/rules/freebayes.rules | 23 ++++++++++++++-----
.../IMAGE_calling/rules/haplotypecaller.rules | 4 ++--
Snakemake/IMAGE_calling/rules/mpileup.rules | 23 ++++++++++++++-----
4 files changed, 40 insertions(+), 15 deletions(-)
diff --git a/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules b/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
index a01e10a..9f7cff3 100644
--- a/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
+++ b/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
@@ -49,4 +49,7 @@ rule GenotypeGVCFs:
mem=config["GenotypeGVCFs"]["mem"]
shell:
- "java -Xmx{params.mem} -jar {config[bin][gatk]} -T GenotypeGVCFs -R {input.ref} --variant {input.gvcf} -o {output} 2> {log}"
+ """
+ java -Xmx{params.mem} -jar {config[bin][gatk]} -T GenotypeGVCFs -R {input.ref} --variant {input.gvcf} -o {output} 2> {log}
+ {config[bin][tabix]} -f -p vcf {output}
+ """
diff --git a/Snakemake/IMAGE_calling/rules/freebayes.rules b/Snakemake/IMAGE_calling/rules/freebayes.rules
index b6b934b..b18e55e 100644
--- a/Snakemake/IMAGE_calling/rules/freebayes.rules
+++ b/Snakemake/IMAGE_calling/rules/freebayes.rules
@@ -32,13 +32,23 @@ rule freebayes_gzip:
"results/freebayes/{sample}.rg.sort.md.real.recal.vcf"
output:
- "results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz.tbi",
- vcf="results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz"
+ temp("results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz")
shell:
"""
- {config[bin][bgzip]} -c {input} > {output.vcf}
- {config[bin][tabix]} -f -p vcf {output.vcf}
+ {config[bin][bgzip]} -c {input} > {output}
+ """
+
+rule freebayes_tabix:
+ input:
+ "results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz"
+
+ output:
+ temp("results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz.tbi")
+
+ shell:
+ """
+ {config[bin][tabix]} -f -p vcf {input}
"""
rule vcf_merge_freebayes:
@@ -47,7 +57,8 @@ rule vcf_merge_freebayes:
vcf=expand("results/freebayes/{sample}.rg.sort.md.real.recal.vcf.gz", sample=all_samples)
output:
- protected("results/freebayes/variants_freebayes_all.vcf.gz")
+ protected("results/freebayes/variants_freebayes_all.vcf.gz.tbi"),
+ vcf=protected("results/freebayes/variants_freebayes_all.vcf.gz")
log:
"results/freebayes/logs/merge_all_samples.stderr"
@@ -55,5 +66,5 @@ rule vcf_merge_freebayes:
shell:
"""
export PATH=`dirname {config[bin][tabix]}`:$PATH
- {config[bin][vcf-merge]} {input.vcf} | {config[bin][bgzip]} -c > {output}; {config[bin][tabix]} -p vcf {output}
+ {config[bin][vcf-merge]} {input.vcf} | {config[bin][bgzip]} -c > {output.vcf}; {config[bin][tabix]} -p vcf {output.vcf}
"""
diff --git a/Snakemake/IMAGE_calling/rules/haplotypecaller.rules b/Snakemake/IMAGE_calling/rules/haplotypecaller.rules
index 40fa56b..ec12ddb 100755
--- a/Snakemake/IMAGE_calling/rules/haplotypecaller.rules
+++ b/Snakemake/IMAGE_calling/rules/haplotypecaller.rules
@@ -16,7 +16,7 @@ rule HaplotypeCaller:
ref=config["reference_genome"]
output:
- gvcf="results/gatk_haplotypecaller/{sample}.rg.sort.md.real.recal.g.vcf.gz",
+ gvcf=protected("results/gatk_haplotypecaller/{sample}.rg.sort.md.real.recal.g.vcf.gz"),
index="results/gatk_haplotypecaller/{sample}.rg.sort.md.real.recal.g.vcf.gz.tbi"
log:
@@ -26,7 +26,7 @@ rule HaplotypeCaller:
params:
mem=config["HaplotypeCaller"]["mem"],
stand_call_conf="30" if config["stand_call_conf"]=="" else config["stand_call_conf"],
- mmq="30" if config["min_mapping_quality"]=="" else config["min_mapping_quality"]
+ mmq="30" if config["min_mapping_quality"]=="" else config["min_mapping_quality"],
mbq="10" if config["min_base_quality"]=="" else config["min_base_quality"]
shell:
diff --git a/Snakemake/IMAGE_calling/rules/mpileup.rules b/Snakemake/IMAGE_calling/rules/mpileup.rules
index 2f17903..8b4e18e 100644
--- a/Snakemake/IMAGE_calling/rules/mpileup.rules
+++ b/Snakemake/IMAGE_calling/rules/mpileup.rules
@@ -32,13 +32,23 @@ rule mpileup_gzip:
"results/mpileup/{sample}.rg.sort.md.real.recal.vcf"
output:
- vcf=protected("results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz"),
- tbi=protected("results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz.tbi")
+ temp("results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz")
shell:
"""
- {config[bin][bgzip]} -c {input} > {output.vcf}
- {config[bin][tabix]} -f -p vcf {output.vcf}
+ {config[bin][bgzip]} -c {input} > {output}
+ """
+
+rule mpileup_tabix:
+ input:
+ "results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz"
+
+ output:
+ temp("results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz.tbi")
+
+ shell:
+ """
+ {config[bin][tabix]} -f -p vcf {input}
"""
rule vcf_merge_mpileup:
@@ -47,7 +57,8 @@ rule vcf_merge_mpileup:
vcf=expand("results/mpileup/{sample}.rg.sort.md.real.recal.vcf.gz", sample=all_samples)
output:
- protected("results/mpileup/variants_mpileup_all.vcf.gz")
+ protected("results/mpileup/variants_mpileup_all.vcf.gz.tbi"),
+ vcf = protected("results/mpileup/variants_mpileup_all.vcf.gz")
log:
"results/mpileup/logs/merge_all_samples.stderr"
@@ -55,6 +66,6 @@ rule vcf_merge_mpileup:
shell:
"""
export PATH=`dirname {config[bin][tabix]}`:$PATH
- {config[bin][vcf-merge]} {input.vcf} | {config[bin][bgzip]} -c > {output} ; {config[bin][tabix]} -p vcf {output}
+ {config[bin][vcf-merge]} {input.vcf} | {config[bin][bgzip]} -c > {output.vcf} ; {config[bin][tabix]} -p vcf {output.vcf}
"""
--
GitLab