Commit 30377015 authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

wilcards fixed

parent d0198660
......@@ -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:
......@@ -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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