gerge with Justin's changes ��branch 'activeDev' of https://github.co…

…m/CCBR/Pipeliner into activeDev
CCBR · Oct 30, 2018 · 2d83f28 · 2d83f28
2 parents c75005e + 22b95b3
commit 2d83f28
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Showing 21 changed files with 507 additions and 264 deletions.
diff --git a/Rules/conpair.rl b/Rules/conpair.rl
@@ -1,6 +1,8 @@
 rule conpair:
     input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
            tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+           normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+           tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
     output: estimate=config['project']['workpath']+"/conpair_out/{x}.conpair",
     params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],genome=config['references'][pfamily]['GENOME'],markersb=config['references'][pfamily]['CONPAIRMARKERSB'],markersa=config['references'][pfamily]['CONPAIRMARKERSA'],rname="pl:conpair"
     shell: "module load conpair; run_gatk_pileup_for_sample.py -B {input.normal} -M {params.markersb} -R {params.genome} -O conpair_out/{params.normalsample}.pileup; run_gatk_pileup_for_sample.py -B {input.tumor} -M {params.markersb} -R {params.genome} -O conpair_out/{params.tumorsample}.pileup; estimate_tumor_normal_contamination.py -T conpair_out/{params.tumorsample}.pileup -N conpair_out/{params.normalsample}.pileup -O {output} -M {params.markersa}"
diff --git a/Rules/gatk.mutect2.rl b/Rules/gatk.mutect2.rl
diff --git a/Rules/gatk.mutect2.tumoronly.rl b/Rules/gatk.mutect2.tumoronly.rl
diff --git a/Rules/index_bams.rl b/Rules/index_bams.rl
@@ -1,6 +1,6 @@
 rule index_bams:
      input:  "{x}.recal.bam"
-     output: out1 = "{x}.recal.bam.bai", out2 = "{x}.recal.bai"
+     output: out1="{x}.recal.bam.bai", out2="{x}.recal.bai"
      params: markdups=config['bin'][pfamily]['INDEXBAM'],rname="pl:indexbam"
-     shell:  "module load samtools/1.9; samtools index {input}; cp {out1} {out2}"
+     shell:  "module load samtools/1.9; samtools index {input}; cp {output.out1} {output.out2}"
 
diff --git a/Rules/manta_germline.rl b/Rules/manta_germline.rl
@@ -1,5 +1,5 @@
 rule manta_germline:
-     input: expand("{x}.recal.bam", x=samples)
+     input: expand("{x}.recal.bam", x=samples),expand("{x}.recal.bam.bai", x=samples)
      output: vcf="manta_out/results/variants/diploidSV.vcf.gz",
              dir="manta_out"
      params: gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta"

diff --git a/Rules/manta_somatic.rl b/Rules/manta_somatic.rl
@@ -1,6 +1,8 @@
 rule manta_somatic:
      input:  normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
              tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+             normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+             tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0], gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta_somatic"
      threads: 8

diff --git a/Rules/manta_somatic_tumoronly.rl b/Rules/manta_somatic_tumoronly.rl
@@ -1,5 +1,6 @@
 rule manta_somatic_tumoronly:
-     input:  tumor=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam"
+     input:  tumor=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam",
+             bai=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam.bai"
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta"
      threads: 8

diff --git a/Rules/manta_wgs.rl b/Rules/manta_wgs.rl
@@ -1,5 +1,5 @@
 rule manta_wgs:
-     input: expand("{x}.recal.bam", x=samples)
+     input: expand("{x}.recal.bam", x=samples),expand("{x}.recal.bam.bai", x=samples)
      output: vcf="manta_out/results/variants/diploidSV.vcf.gz",
              dir="manta_out"
      params: gres="lscratch:100",gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],snpsites=config['references'][pfamily]['SNPSITES'],rname="pl:manta"

diff --git a/Rules/manta_wgs_somatic.rl b/Rules/manta_wgs_somatic.rl
@@ -1,6 +1,8 @@
 rule manta_wgs_somatic:
      input:  normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
              tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+             normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+             tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],genome=config['references'][pfamily]['GENOME'],rname="pl:manta"
      threads: 8

diff --git a/Rules/manta_wgs_somatic_tumoronly.rl b/Rules/manta_wgs_somatic_tumoronly.rl
@@ -1,5 +1,6 @@
 rule manta_wgs_somatic_tumoronly:
      input:  tumor=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam",
+             bai=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam.bai",
      output: vcf="manta_out/{x}/results/variants/candidateSV.vcf.gz",
      params: tumorsample=lambda wildcards: config['project']['units'][wildcards.x],genome=config['references'][pfamily]['GENOME'],rname="pl:manta"
      threads: 8

diff --git a/Rules/mkdir_somatic.rl b/Rules/mkdir_somatic.rl
@@ -1,5 +1,5 @@
 rule mkdir_somatic:
-        input:  expand("{s}.recal.bam", s=samples)
+        input:  expand("{s}.recal.bam", s=samples),expand("{s}.recal.bam.bai", s=samples)
         output: mutect_dir=config['project']['workpath']+"/mutect_out",
                 mutect2_dir=config['project']['workpath']+"/mutect2_out",
                 mut2chrom_dir=config['project']['workpath']+"/mutect2_out/chrom_files",

diff --git a/Rules/mutect.rl b/Rules/mutect.rl
@@ -1,7 +1,9 @@
 rule mutect:
        input:  normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
                tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
-               targets=ancient("exome_targets.bed")
+               targets=ancient("exome_targets.bed"),
+               lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+               lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
        output: vcf=temp(config['project']['workpath']+"/mutect_out/{x}.vcf"),
                stats=config['project']['workpath']+"/mutect_out/{x}.stats.out",
                vcfRename=config['project']['workpath']+"/mutect_out/{x}.FINAL.vcf",

diff --git a/Rules/mutect_wgs.rl b/Rules/mutect_wgs.rl
@@ -1,6 +1,8 @@
 rule mutect_wgs:
        input:  normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
                tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+               normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+               tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
        output: vcf=temp(config['project']['workpath']+"/mutect_out/{x}.vcf"),
                stats=config['project']['workpath']+"/mutect_out/{x}.stats.out",
                vcfRename=config['project']['workpath']+"/mutect_out/{x}.FINAL.vcf",

diff --git a/Rules/somatic.germline.calls.rl b/Rules/somatic.germline.calls.rl
@@ -1,5 +1,6 @@
 rule somatic_germline_calls:
      input:  bams=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam",
+             bai=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam.bai",
              targets=config['project']['workpath']+"/exome_targets.bed"
      output: "{x}.g.vcf"
      params: genome=config['references'][pfamily]['GENOME'],regions="exome_targets.bed",knowns=config['references'][pfamily]['KNOWNVCF2'],snpsites=config['references'][pfamily]['SNPSITES'],gatk=config['bin'][pfamily]['GATK'],rname="pl:germcalls"

diff --git a/Rules/strelka.rl b/Rules/strelka.rl
@@ -1,7 +1,9 @@
 rule strelka:
     input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
            tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
-           targets=ancient("exome_targets.bed")
+           targets=ancient("exome_targets.bed"),
+           lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+           lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
     output: vcf=temp(config['project']['workpath']+"/strelka_out/{x}.vcf"),
             vcffiltered=temp(config['project']['workpath']+"/strelka_out/{x}_filtered.vcf"),
             final=config['project']['workpath']+"/strelka_out/{x}_FINAL.vcf",

diff --git a/Rules/svaba_germline.rl b/Rules/svaba_germline.rl
@@ -1,5 +1,5 @@
 rule svaba_germline:
-     input: expand("{x}.recal.bam", x=samples)
+     input: expand("{x}.recal.bam", x=samples),expand("{x}.recal.bam.bai", x=samples)
      output: config['project']['workpath']+"/svaba_out/svaba.log"
      params: genome=config['references'][pfamily]['CNVKITGENOME'],rname="svaba"
      threads: 32

diff --git a/Rules/svaba_wgs_somatic.rl b/Rules/svaba_wgs_somatic.rl
@@ -1,6 +1,8 @@
 rule svaba_wgs_somatic:
      input:  normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
              tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+             normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+             tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
      output: "svaba_out/{x}.log"
      params: tumorsample=lambda wildcards: config['project']['pairs'][wildcards.x][1],normalsample=lambda wildcards: config['project']['pairs'][wildcards.x][0],genome=config['references'][pfamily]['CNVKITGENOME'],rname="svaba"
      threads: 32

diff --git a/Rules/wgs.somatic.germline.calls.rl b/Rules/wgs.somatic.germline.calls.rl
@@ -1,5 +1,6 @@
 rule somatic_wgs_germline_calls:
-     input:  bams=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam"
+     input:  bams=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam",
+             bai=lambda wildcards: config['project']['units'][wildcards.x]+".recal.bam.bai"
      output: "{x}.g.vcf"
      params: genome=config['references'][pfamily]['GENOME'],regions="exome_targets.bed",knowns=config['references'][pfamily]['KNOWNVCF2'],snpsites=config['references'][pfamily]['SNPSITES'],gatk=config['bin'][pfamily]['GATK'],rname="pl:germcalls"
      threads: 4

diff --git a/Rules/wgs_strelka.rl b/Rules/wgs_strelka.rl
@@ -1,6 +1,8 @@
 rule wgs_strelka:
     input: normal=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam",
            tumor=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam",
+           normalbai=lambda wildcards: config['project']['pairs'][wildcards.x][0]+".recal.bam.bai",
+           tumorbai=lambda wildcards: config['project']['pairs'][wildcards.x][1]+".recal.bam.bai"
     output: vcf=temp(config['project']['workpath']+"/strelka_out/{x}.vcf"),
             vcffiltered=temp(config['project']['workpath']+"/strelka_out/{x}_filtered.vcf"),
             final=config['project']['workpath']+"/strelka_out/{x}_FINAL.vcf",