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Merge branch 'activeDev' of https://github.com/CCBR/Pipeliner into ac…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,9 +1,8 @@ | ||
| rule maftools_tumoronly: | ||
| input: mutect2mafs=expand(config['project']['workpath']+"/mutect2_out/oncotator_out/{s}.maf",s=samples), | ||
| output: mutect2pre=temp(config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants.maf"), | ||
| mutect2fix=temp(config['project']['workpath']+"/mutect2_out/oncotator_out/mutect2_variants_fixed.maf"), | ||
| mutect2maf=config['project']['workpath']+"/mutect2_out/oncotator_out/final_filtered.maf", | ||
| mutect2summary=config['project']['workpath']+"/mutect2_out/mutect2_maf_summary.pdf", | ||
| mutect2oncoprint=config['project']['workpath']+"/mutect2_out/mutect2_oncoplot.pdf", | ||
| params: dir=config['project']['workpath'],rname="pl:maftools" | ||
| shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; perl Scripts/prep_mafs.pl mutect2_out/oncotator_out/mutect2_variants.maf mutect2; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_filtered.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}" | ||
| shell: "cat mutect2_out/oncotator_out/*.maf > mutect2_out/oncotator_out/mutect2_variants.maf; module load R/3.5; Rscript Scripts/maftools.R {params.dir}/mutect2_out/oncotator_out/ mutect2_variants.maf {params.dir}/mutect2_out/mutect2_maf_summary.pdf {output.mutect2oncoprint}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,12 +1,5 @@ | ||
| rule mkdir_somatic: | ||
| 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", | ||
| cnvkit_dir=config['project']['workpath']+"/cnvkit_out", | ||
| strelka_dir=config['project']['workpath']+"/strelka_out", | ||
| theta_dir=config['project']['workpath']+"/theta_out", | ||
| conpair_dir=config['project']['workpath']+"/conpair_out", | ||
| manta_dir=config['project']['workpath']+"/manta_out" | ||
| output: temp("QC/decoy") | ||
| params: rname="pl:mkdir" | ||
| shell: "mkdir -p strelka_out; mkdir -p strelka_out/oncotator_out; mkdir -p strelka_out/mutsigCV_out; mkdir -p cnvkit_out; mkdir -p mutect_out; mkdir -p mutect_out/oncotator_out; mkdir -p mutect_out/mutsigCV_out; mkdir -p theta_out; mkdir -p conpair_out; mkdir -p germline_vcfs; mkdir -p mutect2_out; mkdir -p mutect2_out/oncotator_out; mkdir -p mutect2_out/mutsigCV_out; mkdir -p mutect2_out/chrom_files; mkdir -p manta_out" | ||
| shell: "echo \'decoy\' > {output}; mkdir -p strelka_out; mkdir -p strelka_out/oncotator_out; mkdir -p strelka_out/mutsigCV_out; mkdir -p cnvkit_out; mkdir -p mutect_out; mkdir -p mutect_out/oncotator_out; mkdir -p mutect_out/mutsigCV_out; mkdir -p theta_out; mkdir -p conpair_out; mkdir -p germline_vcfs; mkdir -p mutect2_out; mkdir -p mutect2_out/oncotator_out; mkdir -p mutect2_out/mutsigCV_out; mkdir -p mutect2_out/chrom_files; mkdir -p manta_out" |
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