fixed map files 4 chrs

Snakefile_para_gatk_PEmerged.smk

@@ -382,11 +382,13 @@ rule gatk4_ref_dict:
     output:
         dic  = "{refp}/{ref}.dict".format(refp=config["REFPATH"],ref=config["GENOME"]) #config["REFPATH"] + "/" + config["GENOME"] +".dict"
     params:
+        refp = config["REFPATH"],
         bind = config["BIND"],
         samtools_bin = config["samtools_bin"],
         gatk4_bin = config["gatk4_bin"]
     shell:
         """
+        rm -f {params.refp}/*.dict
         singularity exec {params.bind} {params.gatk4_bin} gatk CreateSequenceDictionary -R {input.ref}
         #singularity exec {params.bind} {params.samtools_bin} samtools faidx {input.ref}
         singularity exec {params.bind} {params.samtools_bin} samtools dict -o {output.dic} {input.ref}
@@ -432,7 +434,7 @@ rule gatk4_gvcf_map_file:
         gvcfmap      = "{outdir}/variant/gvcf_{{mychr}}_list.map".format(outdir=config["outdir"]),
     params:
         ch="{mychr}",
-        csv         = expand("{sample}\t{outdir}/variant/gatk_gvcf/{sample}-{{mychr}}.g.vcf.gz", outdir=config["outdir"], sample=samples['SampleName']),
+        csv         = expand("{sample}\t{outdir}/variant/gatk_gvcf/{sample}", outdir=config["outdir"], sample=samples['SampleName']),
         bamsp       = "{outdir}/mapped".format(outdir=config["outdir"]),
         outlist     = config["outdir"]
     threads: 1
@@ -440,7 +442,7 @@ rule gatk4_gvcf_map_file:
         x=params.csv
         f = open(output.gvcfmap, "w")
         for i in x:
-            f.write("%s\n" % (i))
+            f.write("{}-{}.g.vcf.gz\n".format(i,params.ch))
         f.close()