Commit d0198660 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

chrs correction

parent d746ea48
......@@ -69,7 +69,7 @@ rule final_outs:
"{outdir}/multiqc/multiqc_report_fastqc.html".format(outdir=config["outdir"]),
"{outdir}/multiqc/multiqc_report_bam.html".format(outdir=config["outdir"]),
#expand("{outdir}/variant/gatk_{mychr}.vcf.gz", outdir=config["outdir"], mychr=CHRS),
#expand("{outdir}/variant/gatk_gvcf/{sample}-{mychr}.g.vcf.gz",outdir=config["outdir"], sample=samples['SampleName'], mychr=CHRS),
#expand("{outdir}/variant/gatk_gvcf/{sample}.{mychr}.g.vcf.gz",outdir=config["outdir"], sample=samples['SampleName'], mychr=CHRS),
#expand("{outdir}/variant/gatk_genomicsdb_{mychr}.ok",outdir=config["outdir"], mychr=CHRS),
#expand("{outdir}/variant/gatk_{mychr}_genotyped.vcf.gz",outdir=config["outdir"], mychr=CHRS),
#"{outdir}/variant/gatk_all.vcf.gz".format(outdir=config["outdir"]),
......@@ -307,8 +307,8 @@ rule gatk4_hc:
bambai = "{outdir}/mapped/{{sample}}_sorted.bam.bai".format(outdir=config["outdir"]),
refdict = "{refp}/{ref}.dict".format(refp=config["REFPATH"],ref=config["GENOME"]),
output:
gvcf="{outdir}/variant/gatk_gvcf/{{sample}}-{{mychr}}.g.vcf.gz".format(outdir=config["outdir"]),
gtbi="{outdir}/variant/gatk_gvcf/{{sample}}-{{mychr}}.g.vcf.gz.tbi".format(outdir=config["outdir"])
gvcf="{outdir}/variant/gatk_gvcf/{{sample}}.{{mychr}}.g.vcf.gz".format(outdir=config["outdir"]),
gtbi="{outdir}/variant/gatk_gvcf/{{sample}}.{{mychr}}.g.vcf.gz.tbi".format(outdir=config["outdir"])
params:
ch="{mychr}",
ref = config["REFPATH"] + "/" + config["GENOME"],
......@@ -330,8 +330,8 @@ rule gatk4_hc:
# 3-3) Generate a map (text file) of gvcf files for each chr
rule gatk4_gvcf_map_file:
input:
gvcfs = expand("{outdir}/variant/gatk_gvcf/{sample}-{{mychr}}.g.vcf.gz", outdir=config["outdir"], sample=samples['SampleName']),
gtbi = expand("{outdir}/variant/gatk_gvcf/{sample}-{{mychr}}.g.vcf.gz.tbi", outdir=config["outdir"], sample=samples['SampleName']),
gvcfs = expand("{outdir}/variant/gatk_gvcf/{sample}.{{mychr}}.g.vcf.gz", outdir=config["outdir"], sample=samples['SampleName']),
gtbi = expand("{outdir}/variant/gatk_gvcf/{sample}.{{mychr}}.g.vcf.gz.tbi", outdir=config["outdir"], sample=samples['SampleName']),
fai = "{refp}/{ref}".format(refp=config["REFPATH"],ref=config["GENOME_FAI"]),
refdict = "{refp}/{ref}.dict".format(refp=config["REFPATH"],ref=config["GENOME"]),
output:
......@@ -346,7 +346,7 @@ rule gatk4_gvcf_map_file:
x=params.csv
f = open(output.gvcfmap, "w")
for i in x:
f.write("{}-{}.g.vcf.gz\n".format(i,params.ch))
f.write("{}.{}.g.vcf.gz\n".format(i,params.ch))
f.close()
......@@ -354,8 +354,8 @@ rule gatk4_gvcf_map_file:
# see: https://gatk.broadinstitute.org/hc/en-us/articles/360040096732-GenomicsDBImport
rule gatk4_gdb:
input:
gvcf = expand("{outdir}/variant/gatk_gvcf/{sample}-{{mychr}}.g.vcf.gz",outdir=config["outdir"],sample=samples['SampleName']),
gtbi = expand("{outdir}/variant/gatk_gvcf/{sample}-{{mychr}}.g.vcf.gz.tbi",outdir=config["outdir"],sample=samples['SampleName']),
gvcf = expand("{outdir}/variant/gatk_gvcf/{sample}.{{mychr}}.g.vcf.gz",outdir=config["outdir"],sample=samples['SampleName']),
gtbi = expand("{outdir}/variant/gatk_gvcf/{sample}.{{mychr}}.g.vcf.gz.tbi",outdir=config["outdir"],sample=samples['SampleName']),
gvcfmap = "{outdir}/variant/gvcf_{{mychr}}_list.map".format(outdir=config["outdir"]),
output:
"{outdir}/variant/gatk_genomicsdb_{{mychr}}.ok".format(outdir=config["outdir"])
......
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