wilcards fixed

Snakefile_para_gatk_SE.smk

@@ -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"])