commands.txt

## Commands
 This section lists commands run by the PURPLE workflow
 
 ### Run AMBER 
  
      ~{amberScript} \
        -reference ~{normal_name} -reference_bam ~{normal_bam} \
        -tumor ~{tumour_name} -tumor_bam ~{tumour_bam} \
        -output_dir ~{tumour_name}.amber/ \
        -loci ~{PON} \
        -ref_genome_version ~{genomeVersion}
  
  ### Run COBALT 
  
      ~{colbaltScript} \
        -reference ~{normal_name} -reference_bam ~{normal_bam} \
        -tumor ~{tumour_name} -tumor_bam ~{tumour_bam} \
        -output_dir ~{tumour_name}.cobalt/ \
        -gc_profile ~{gcProfile} \
        -pcf_gamma ~{gamma}
  
  ### Filter structural variant VCFs using GRIPSS, this is optional but recommended
  
      ~{gripssScript} \
          -vcf ~{vcf}  \
          -sample ~{tumour_name} -reference ~{normal_name} \
          -ref_genome_version ~{genomeVersion} \
          -ref_genome ~{refFasta} \
          -pon_sgl_file ~{pon_sgl_file} \
          -pon_sv_file ~{pon_sv_file} \
          -known_hotspot_file ~{known_hotspot_file} \
          -repeat_mask_file ~{repeat_mask_file} \
          -output_dir gripss/ \
          -hard_min_tumor_qual ~{hard_min_tumor_qual} \
          ~{filter_sgls}
  
  ### Filter small variant (SNV + in/del) VCFs using bcftools, this is optional but recommended
  
       ~{bcftoolsScript} view -f "PASS" -S samples.txt -r ~{regions} ~{difficultRegions} ~{vcf} |\
       ~{bcftoolsScript} norm --multiallelics - --fasta-ref ~{genome} |\
       ~{bcftoolsScript} filter -i "(FORMAT/AD[0:1])/(FORMAT/AD[0:0]+FORMAT/AD[0:1]) >= ~{tumorVAF}"  > ~{tumour_name}.PASS.vcf
  
  ### Run PURPLE 
  
      ~{purpleScript} \
        -ref_genome_version ~{genomeVersion} \
        -ref_genome ~{refFasta}  \
        -gc_profile ~{gcProfile} \
        -ensembl_data_dir ~{ensemblDir}  \
        -reference ~{normal_name} -tumor ~{tumour_name}  \
        -amber ~{tumour_name}.amber -cobalt ~{tumour_name}.cobalt \
        ~{"-somatic_sv_vcf " + SV_vcf} \
        ~{"-somatic_vcf " + smalls_vcf} \
        -output_dir ~{tumour_name}.purple \
        -no_charts
  
  ### Run LINX, if structural variant calls from GRIDSS are included
  
      ~{linxScript} \
        -sample ~{tumour_name} \
        -ref_genome_version ~{genomeVersion} \
        -ensembl_data_dir ~{ensemblDir}  \
        -check_fusions \
        -known_fusion_file ~{fusions_file} \
        -purple_dir ~{tumour_name}.purple \
        -output_dir ~{tumour_name}.linx