Commit 44b422fc authored by Jacques Lagnel's avatar Jacques Lagnel
Browse files

wilcards fixed

parent 0187c2d5
......@@ -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"],
......
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