chrs correction

Snakefile_para_gatk_SE.smk

@@ -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"])