@prefix LoadListingRequirement: . @prefix SchemaDefRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix cwl: . @prefix ResourceRequirement: . cwl:source ; cwl:valueFrom "${\n if(self){\n for(var i=0; i cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:inputBinding [ CommandLineBinding:position -5 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.snvs.vcf.gz" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "Add snv and indel bam-readcount files to a vcf" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:default 1e-01 ; cwl:inputBinding [ CommandLineBinding:position 6 ] ; sld:type xsd:float , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "mutect.filtered.vcf.gz" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:default "TUMOR" . cwl:source . cwl:valueFrom "mutect" . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "docm_filtered_variants.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.prefix).annotated.tsv" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated.af_filtered.vcf" ] ; sld:type cwl:File . cwl:default 1e-03 ; sld:type xsd:float , sld:null . cwl:default "ALT" , "REF" , "CHROM" , "set" , "AC" , "AF" , "POS" , "ID" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default "select_variants" ; sld:type xsd:string , sld:null . cwl:source . sld:type . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_snv.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--bam-file" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default false ; sld:type xsd:boolean , sld:null . cwl:default 1 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run . cwl:default false ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--coding_only" ] ; sld:type xsd:boolean . rdfs:comment "custom type, check types directory for input format" ; sld:type [ sld:items ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.file.basename).gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.vcf.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Custom allele frequency filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(inputs.vcf.path)" ] [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] "/usr/bin/perl" "/opt/vep/src/ensembl-vep/filter_vep" "--format" "vcf" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.af_filtered.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/vcf_check.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "add VEP annotation to report" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.prefix).annotated.tsv" ] ) ; cwl:baseCommand ( "vep-annotation-reporter" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . cwl:outputSource ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "varscan somatic workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , . sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "*.interval_list" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "mapq_filtered.vcf.gz" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:linkMerge "merge_flattened" ; cwl:source , . cwl:default "merged" ; sld:type xsd:string , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:inputBinding [ CommandLineBinding:position -6 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . rdfs:comment "Previously discovered variants to be flagged in this workflow's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:in , ; cwl:out ; cwl:run . sld:type cwl:File . sld:type xsd:string . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:Workflow ; rdfs:label "Detect Variants workflow for WGS pipeline" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ; cwl:outputs , , , , , , , , , , , , , , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] . cwl:default true . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--fasta" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "output.indel.vcf" ] ; sld:type cwl:File . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "known_variants_filtered.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:default 400 ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: 'homo_sapiens' or 'mus_musculus'" ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "--species" ] ; sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--mask" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "Each variant in this file that is also in the above file (if supplied) will be marked with a PREVIOUSLY_DISCOVERED flag in its INFO field" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:default "TUMOR" . cwl:default 9.9e-01 ; sld:type xsd:float , sld:null . cwl:in , , ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:valueFrom "annotated_filtered.vcf" . cwl:source . a cwl:CommandLineTool ; rdfs:label "run bam-readcount" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:baseCommand ( "/usr/bin/python" "bam_readcount_helper.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bam_readcount_helper-cwl:1.1.1" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/env python\n\nimport sys\nimport os\nfrom cyvcf2 import VCF\nimport tempfile\nimport csv\nfrom subprocess import Popen, PIPE\n\ndef generate_region_list(hash):\n fh = tempfile.NamedTemporaryFile('w', delete=False)\n writer = csv.writer(fh, delimiter='\\t')\n for chr, positions in hash.items():\n for pos in sorted(positions.keys()):\n writer.writerow([chr, pos, pos])\n fh.close()\n return fh.name\n\ndef filter_sites_in_hash(region_list, bam_file, ref_fasta, prefixed_sample, output_dir, insertion_centric, map_qual, base_qual):\n bam_readcount_cmd = ['/usr/bin/bam-readcount', '-f', ref_fasta, '-l', region_list, '-w', '0', '-b', str(base_qual), '-q', str(map_qual)]\n if insertion_centric:\n bam_readcount_cmd.append('-i')\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n else:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n bam_readcount_cmd.append(bam_file)\n execution = Popen(bam_readcount_cmd, stdout=PIPE, stderr=PIPE)\n stdout, stderr = execution.communicate()\n if execution.returncode == 0:\n with open(output_file, 'wb') as output_fh:\n output_fh.write(stdout)\n else:\n sys.exit(stderr)\n\n#initializing these with default values\nmin_base_qual = 20\nmin_mapping_qual = 0\n\nif len(sys.argv) == 7:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir)= sys.argv\nelif len(sys.argv) == 8:\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual)= sys.argv\nelif len(sys.argv) == 9: #elif instead of else for explicit safety\n (script_name, vcf_filename, sample, ref_fasta, bam_file, prefix, output_dir, min_base_qual, min_mapping_qual)= sys.argv\n\nif prefix == 'NOPREFIX':\n prefixed_sample = sample\nelse:\n prefixed_sample = '_'.join([prefix, sample])\n\nvcf_file = VCF(vcf_filename)\nsample_index = vcf_file.samples.index(sample)\n\nrc_for_indel = {}\nrc_for_snp = {}\nfor variant in vcf_file:\n ref = variant.REF\n chr = variant.CHROM\n start = variant.start\n end = variant.end\n pos = variant.POS\n for var in variant.ALT:\n if len(ref) > 1 or len(var) > 1:\n #it's an indel or mnp\n if len(ref) == len(var) or (len(ref) > 1 and len(var) > 1):\n sys.stderr.write(\"Complex variant or MNP will be skipped: %s\\t%s\\t%s\\t%s\\n\" % (chr, pos, ref , var))\n continue\n elif len(ref) > len(var):\n #it's a deletion\n pos += 1\n unmodified_ref = ref\n ref = unmodified_ref[1]\n var = \"-%s\" % unmodified_ref[1:]\n else:\n #it's an insertion\n var = \"+%s\" % var[1:]\n if chr not in rc_for_indel:\n rc_for_indel[chr] = {}\n if pos not in rc_for_indel[chr]:\n rc_for_indel[chr][pos] = {}\n if ref not in rc_for_indel[chr][pos]:\n rc_for_indel[chr][pos][ref] = {}\n rc_for_indel[chr][pos][ref] = variant\n else:\n #it's a SNP\n if chr not in rc_for_snp:\n rc_for_snp[chr] = {}\n if pos not in rc_for_snp[chr]:\n rc_for_snp[chr][pos] = {}\n if ref not in rc_for_snp[chr][pos]:\n rc_for_snp[chr][pos][ref] = {}\n rc_for_snp[chr][pos][ref] = variant\n\nif len(rc_for_snp.keys()) > 0:\n region_file = generate_region_list(rc_for_snp)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, False, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_snv.tsv')\n open(output_file, 'w').close()\n\nif len(rc_for_indel.keys()) > 0:\n region_file = generate_region_list(rc_for_indel)\n filter_sites_in_hash(region_file, bam_file, ref_fasta, prefixed_sample, output_dir, True, min_mapping_qual, min_base_qual)\nelse:\n output_file = os.path.join(output_dir, prefixed_sample + '_bam_readcount_indel.tsv')\n open(output_file, 'w').close()\n" ; cwl:entryname "bam_readcount_helper.py" ] ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 16000 ] ; cwl:stdout "$(inputs.sample)_bam_readcount.tsv" . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "docm_raw_variants.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:source . sld:type xsd:string . rdfs:label "Used as key for new VEP annotation" ; sld:type xsd:string . sld:type xsd:string . cwl:in , , , , ; cwl:out ; cwl:run . cwl:default "indel" . sld:type . cwl:in ; cwl:out ; cwl:run . sld:type xsd:int . cwl:default "NOPREFIX" ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type xsd:string , sld:null . a cwl:CommandLineTool ; rdfs:label "filter vcf for variants with high percentage of mapq0 reads" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/bin/bash" "/usr/bin/mapq0_vcf_filter.sh" [ cwl:valueFrom "$(runtime.outdir)/mapq_filtered.vcf.gz" ] ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/mapq0-filter:v0.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ; ResourceRequirement:tmpdirMin 10000 ] . rdfs:label "Use this annotation for gnomad filtering?" ; sld:type xsd:boolean , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.hc.vcf" ] ; sld:type cwl:File . cwl:source . rdfs:comment "Sample name to be replaced" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . sld:type xsd:int , sld:null . rdfs:comment "ensembl version - Must be present in the cache directory. Example: '95'" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "--cache_version" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:float . sld:type cwl:File . rdfs:comment "vcf file to filter" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . sld:type cwl:File . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "somatic_llr_filtered.vcf" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "vcf merge" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "--allow-overlaps" "--remove-duplicates" "--output-type" "z" "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.merged_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "concat" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "interval_list.bed" ] ; sld:type cwl:File . sld:type xsd:string . sld:type xsd:string . sld:type cwl:File . cwl:source . cwl:source . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "strelka workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated_filtered.vcf" ] ; sld:type cwl:File . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:default "snv" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--tumorBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:label "File to be used for annotation, include index file" ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Filter variants from the DoCM detector" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.outdir)/docm_filtered_variants.vcf" ) ; cwl:baseCommand ( "/usr/bin/perl" "docm_filter.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.4.2" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse feature qw(say);\n\ndie(\"Wrong number of arguments. Provide docm_vcf, normal_cram, tumor_cram, output_vcf_file, set_filter_flag\") unless scalar(@ARGV) == 5;\nmy ($docm_vcf, $normal_cram, $tumor_cram, $output_vcf_file, $set_filter_flag) = @ARGV;\n\nmy $samtools = '/opt/samtools/bin/samtools';\nmy $normal_header_str = `$samtools view -H $normal_cram`;\nmy $tumor_header_str = `$samtools view -H $tumor_cram`;\n\nmy ($normal_name) = $normal_header_str =~ /SM:([ -~]+)/;\nmy ($tumor_name) = $tumor_header_str =~ /SM:([ -~]+)/;\n\nunless ($normal_name and $tumor_name) {\n die \"Failed to get normal_name: $normal_name from $normal_cram AND tumor_name: $tumor_name from $tumor_cram\";\n}\n\nmy $docm_vcf_fh;\nif($docm_vcf =~ /.gz$/){\n open($docm_vcf_fh, \"gunzip -c $docm_vcf |\") or die(\"couldn't open $docm_vcf to read\");\n} else {\n open($docm_vcf_fh, $docm_vcf) or die(\"couldn't open $docm_vcf to read\");\n}\nopen(my $docm_out_fh, \">\", \"$output_vcf_file\") or die(\"couldn't open $output_vcf_file for write\");\n\nmy ($normal_index, $tumor_index);\n\nwhile (<$docm_vcf_fh>) {\n chomp;\n if (/^##/) {\n say $docm_out_fh $_;\n }\n elsif (/^#CHROM/) {\n if ($set_filter_flag) {\n say $docm_out_fh '##FILTER=';\n }\n my @columns = split /\\t/, $_;\n my %index = (\n $columns[9] => 9,\n $columns[10] => 10,\n );\n ($normal_index, $tumor_index) = map{$index{$_}}($normal_name, $tumor_name);\n unless ($normal_index and $tumor_index) {\n die \"Failed to get normal_index: $normal_index for $normal_name AND tumor_index: $tumor_index for $tumor_name\";\n }\n $columns[9] = $normal_name;\n $columns[10] = $tumor_name;\n my $header = join \"\\t\", @columns;\n say $docm_out_fh $header;\n }\n else {\n my @columns = split /\\t/, $_;\n my @tumor_info = split /:/, $columns[$tumor_index];\n my ($AD, $DP) = ($tumor_info[1], $tumor_info[2]);\n next unless $AD;\n my @AD = split /,/, $AD;\n shift @AD; #the first one is ref count\n \n for my $ad (@AD) {\n if ($ad > 5 and $ad/$DP > 0.01) {\n my ($normal_col, $tumor_col) = map{$columns[$_]}($normal_index, $tumor_index);\n $columns[9] = $normal_col;\n $columns[10] = $tumor_col;\n if ($set_filter_flag) {\n $columns[6] = 'DOCM_ONLY';\n }\n else {\n $columns[6] = '.';\n }\n my $new_line = join \"\\t\", @columns;\n say $docm_out_fh $new_line;\n last;\n }\n }\n }\n}\n\nclose($docm_vcf_fh);\nclose($docm_out_fh);\n" ; cwl:entryname "docm_filter.pl" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "filter" ] ; sld:type xsd:boolean . cwl:default "Consequence" , "Feature" , "SYMBOL" , "HGVSp" , "HGVSc" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in , ; cwl:out ; cwl:run . cwl:default "NORMAL" . a cwl:Workflow ; rdfs:label "Varscan Workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , , , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . sld:type xsd:boolean . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source ; cwl:valueFrom "$(self)_full" . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:default 8 ; sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:in , , , , , , , , , , , ; cwl:out ; cwl:run . cwl:source ; cwl:valueFrom "$(self)_filtered" . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(\"renamed.\" + inputs.input_vcf.basename)" ] ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/usr/bin/perl" "intervals_to_bed.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use feature qw(say);\n\nfor my $line (<>) {\n chomp $line;\n\n next if substr($line,0,1) eq '@'; #skip header lines\n\n my ($chrom, $start, $stop) = split(/\\t/, $line);\n say(join(\"\\t\", $chrom, $start-1, $stop));\n}\n" ; cwl:entryname "intervals_to_bed.pl" ] ] ; cwl:stdout "interval_list.bed" . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "decomposed.vcf.gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf" ] ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] ; sld:type [ rdfs:label "Require exact or overlap to annotate variants" ; sld:symbols , ; sld:type sld:enum ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "filter variants at sites below a given sequence depth in each sample" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(runtime.outdir)/depth_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/depth_filter.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/depth-filter:0.1.2" ] . cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-s" ] ; sld:type xsd:string , sld:null . cwl:source , . cwl:source . cwl:source . cwl:in , , ; cwl:out ; cwl:run . sld:fields , , , , , ; sld:type sld:record . sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.name)" ] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Mutect2 (GATK 4)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "mutect.vcf.gz" ] ) ; cwl:baseCommand ( "/bin/bash" "Mutect2.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 32000 ; ResourceRequirement:tmpdirMin 100000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -o pipefail\nset -o errexit\n\nexport tumor_bam=\"$3\"\nexport normal_bam=\"$4\"\n\nTUMOR=`perl -e 'my $header_str = qx(samtools view -H $ENV{tumor_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the TUMOR bam.\nNORMAL=`perl -e 'my $header_str = qx(samtools view -H $ENV{normal_bam}); my ($sample_name) = $header_str =~ /SM:([ -~]+)/; print $sample_name'` #Extracting the sample name from the NORMAL bam.\n/gatk/gatk Mutect2 --java-options \"-Xmx20g\" -O $1 -R $2 -I $3 -tumor \"$TUMOR\" -I $4 -normal \"$NORMAL\" -L $5 #Running Mutect2.\n/gatk/gatk FilterMutectCalls -R $2 -V mutect.vcf.gz -O mutect.filtered.vcf.gz #Running FilterMutectCalls on the output vcf.\n" ; cwl:entryname "Mutect2.sh" ] ] . a cwl:CommandLineTool ; rdfs:label "HaplotypeCaller (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-gt_mode" "GENOTYPE_GIVEN_ALLELES" "-o" [ cwl:valueFrom "$(runtime.outdir)/docm_raw_variants.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "HaplotypeCaller" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] . sld:type cwl:File . cwl:default "AD" , "AF" , "DP" , "GT" ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-GF" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:valueFrom "varscan" . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "Wildtype" , "Downstream" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default 5 ; sld:type xsd:float , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--reference" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf" ] ; sld:type cwl:File . cwl:in , ; cwl:out , , , , , ; cwl:run . sld:type xsd:string . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:CommandLineTool ; rdfs:label "Ensembl Variant Effect Predictor" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--format" "vcf" "--vcf" "--fork" "4" "--term" "SO" "--transcript_version" "--offline" "--cache" "--symbol" "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "-I" "/opt/lib/perl/VEP/Plugins" "/usr/bin/variant_effect_predictor.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SchemaDefRequirement ; SchemaDefRequirement:types ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/vep_helper-cwl:1.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 64000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:outputBinding [ CommandOutputBinding:glob "output.snp.vcf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "results/variants/somatic.indels.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:string . cwl:source . rdfs:label "Annotation file type" ; sld:symbols , , , , ; sld:type sld:enum . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-i" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: 'GRCh38' or 'GRCm38'" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--assembly" ] ; sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(runtime.outdir)/$(self.basename)" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-I" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.merged_vcf_basename).vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:in , , ; cwl:out ; cwl:run . cwl:in , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--excludeFiltered" ] ; sld:type xsd:boolean , sld:null . sld:type xsd:float , sld:null . sld:type xsd:float , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:label "Adds an INFO tag (PREVIOUSLY_DISCOVERED) flagging variants in the target vcf present in a known-variants file" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-Oz" "-o" "known_variants_filtered.vcf.gz" ) ; cwl:baseCommand ( "/opt/bcftools/bin/bcftools" "annotate" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] . sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "mutect,varscan,strelka" "-o" [ cwl:valueFrom "$(runtime.outdir)/combined.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] . sld:type sld:null ; sld:type [ rdfs:label "custom type, check types directory for input format" ; cwl:inputBinding [ CommandLineBinding:position 6 ; cwl:valueFrom "${\n return [self.annotation.check_existing ? '--check_existing' : '',\n '--custom',\n [self.annotation.file.path,\n self.annotation.name,\n self.annotation.data_format,\n self.method,\n self.force_report_coordinates ? 1 : 0,\n self.annotation.vcf_fields ? self.annotation.vcf_fields : ''\n ].filter(String).join(',')\n ].filter(String)\n}\n" ] ; sld:items ; sld:type sld:array ] . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.hc.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--tumor-sample-name" ] ; sld:type xsd:string . cwl:default "ID" , "ALT" , "CHROM" , "POS" , "REF" , "set" ; cwl:inputBinding [ CommandLineBinding:position 3 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "-F" ] ; sld:items xsd:string ; sld:type sld:array ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_vcf_basename).vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 5e-02 ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--min-var-freq" ] ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . rdfs:comment "Previously discovered variants to be flagged in this pipelines's output vcf" ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:Workflow ; rdfs:label "mutect parallel workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--alleles" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 1.5e-01 ; sld:type xsd:float , sld:null . cwl:in , , , , , , , , ; cwl:out , , , ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:in , , ; cwl:out ; cwl:run . cwl:source . sld:type [ sld:symbols , ; sld:type sld:enum ] ; sld:type [ sld:symbols , ; sld:type sld:enum ] . sld:type xsd:boolean . cwl:default 0 ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.hc.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n return [\n \"--filter\",\n [\n inputs.field_name, \"<\", inputs.maximum_population_allele_frequency,\n \"or not\", inputs.field_name\n ].join(\" \")\n ]\n}\n" ] ; sld:type xsd:float . a cwl:CommandLineTool ; rdfs:label "create filtered VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:arguments ( "--maskName" "processSomatic" "--filterNotInMask" "-o" [ cwl:valueFrom "$(runtime.outdir)/output.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantFiltration" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type [ cwl:inputBinding [ CommandLineBinding:prefix "--plugin" ] ; sld:items xsd:string ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--allowMissingData" "-o" [ cwl:valueFrom "$(runtime.outdir)/variants.tsv" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "VariantsToTable" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:source . cwl:source . cwl:source . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Somatic.vcf" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:mutect" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "merged.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n if(inputs.vcf.nameext.equals(\".gz\")){\n return inputs.vcf.nameroot.replace(/.vcf$/, \"\") + \".sanitized.vcf.gz\";\n }\n return inputs.vcf.nameroot + \".sanitized.vcf.gz\";\n}\n" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -3 ; CommandLineBinding:prefix "--minimum_depth" ] ; sld:type xsd:int . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . sld:type xsd:int , sld:null . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:source . a cwl:CommandLineTool ; rdfs:label "CombineVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "-genotypeMergeOptions" "PRIORITIZE" "--rod_priority_list" "callers,docm" "--setKey" "null" "-o" [ cwl:valueFrom "$(runtime.outdir)/merged.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "CombineVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle" ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "add_gt.vcf" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:default "NORMAL" . cwl:source . a cwl:CommandLineTool ; rdfs:label "run vt decompose" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:arguments ( "-s" "-o" [ cwl:valueFrom "$(runtime.outdir)/decomposed.vcf.gz" ] ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:baseCommand ( "vt" "decompose" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "quay.io/biocontainers/vt:0.57721--hf74b74d_1" ] . sld:type xsd:boolean , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--normalBam=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . rdfs:comment "genome assembly to use in vep. Examples: GRCh38 or GRCm38" ; sld:type xsd:string . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:default "flag_pick" ; cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--" ; CommandLineBinding:separate false ] ; sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:default "DNA" . cwl:source . cwl:source . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; cwl:outputBinding [ CommandOutputBinding:glob "${\n var name = \"_bam_readcount_indel.tsv\";\n if (inputs.prefix.equals(\"NOPREFIX\")) {\n name = inputs.sample + name;\n }\n else {\n name = inputs.prefix + \"_\" + inputs.sample + name;\n }\n return name;\n}\n" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "use the binomial/llr somatic filter to weed out low confidence variants" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--overwrite" [ cwl:valueFrom "$(runtime.outdir)/somatic_llr_filtered.vcf" ] ) ; cwl:baseCommand ( "/opt/conda/bin/python3" "/usr/bin/somatic_llr_filter.py" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/somatic-llr-filter:v0.4.3" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:in , , , , , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "strelka 2.9.9" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "$(inputs.cpu_reserved)" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docker_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/strelka-cwl:2.9.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 4000 ] . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "process VCF workflow" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs . rdfs:label "List of VCF fields to annotate" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "False Positive filter" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:arguments ( "--bam-readcount" "/usr/bin/bam-readcount" "--samtools" "/opt/samtools/bin/samtools" "--output" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/fpfilter.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/fp_filter-cwl:1.0.1" ] . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . a cwl:Workflow ; rdfs:label "Detect Docm variants" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 somatic" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "varscan_helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\n\nset -o errexit\nset -o nounset\n\nif [ $# -lt 7 ]\nthen\n echo \"Usage: $0 [TUMOR_BAM] [NORMAL_BAM] [REFERENCE] [STRAND_FILTER] [MIN_COVERAGE] [MIN_VAR_FREQ] [P_VALUE] [roi_bed?]\"\n exit 1\nfi\n\nTUMOR_BAM=\"$1\"\nNORMAL_BAM=\"$2\"\nREFERENCE=\"$3\"\nSTRAND_FILTER=\"$4\"\nMIN_COVERAGE=\"$5\"\nMIN_VAR_FREQ=\"$6\"\nP_VALUE=\"$7\"\nOUTPUT=\"${HOME}/output\"\n\nif [ -z ${8+x} ]\nthen\n #run without ROI\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nelse\n ROI_BED=\"$8\"\n java -jar /opt/varscan/VarScan.jar somatic \\\n <(/opt/samtools/bin/samtools mpileup --no-baq -l \"$ROI_BED\" -f \"$REFERENCE\" \"$NORMAL_BAM\" \"$TUMOR_BAM\") \\\n $OUTPUT \\\n --strand-filter $STRAND_FILTER \\\n --min-coverage $MIN_COVERAGE \\\n --min-var-freq $MIN_VAR_FREQ \\\n --p-value $P_VALUE \\\n --mpileup 1 \\\n --output-vcf\nfi\n" ; cwl:entryname "varscan_helper.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 12000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--exome" ] ; sld:type xsd:boolean . cwl:default "NORMAL" . cwl:source . cwl:source . rdfs:comment "Sample name to replace the other" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type xsd:string . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "variants.tsv" ] ; sld:type cwl:File . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--variant:strelka" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:in , , , , , ; cwl:out ; cwl:run . cwl:default "AD" , "GT" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:default "fpfilter" ; sld:type xsd:string , sld:null . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant:callers" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "A vcf of previously discovered variants to be marked in the second input vcf; if not provided, this tool does nothing but rename the second input vcf" ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n return [ '-a', self.path, '-m', 'PREVIOUSLY_DISCOVERED' ];\n}\n" ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus" ; sld:type xsd:string . cwl:source . cwl:in , , , , ; cwl:out ; cwl:run . sld:type xsd:float . cwl:default 8 ; cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--referenceFasta=" ; CommandLineBinding:separate false ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:baseCommand ( "/bin/bash" "rename_sample.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bcftools-cwl:1.9" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 8000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/bin/bash\nset -eou pipefail\nbasen=`basename \"$3\"`\nbasen=\"renamed.$basen\"\n\n#escape spaces, otherwise bcftools will try to use them as a delimiter\n#triple backslash to escape within backticks and then again within sed\nold_name=`echo \"$1\" | sed 's/ /\\\\\\ /g'`\nnew_name=`echo \"$2\" | sed 's/ /\\\\\\ /g'`\n\necho \"$old_name $new_name\" > sample_update.txt\n/opt/bcftools/bin/bcftools reheader -s sample_update.txt -o \"$basen\" \"$3\"\n" ; cwl:entryname "rename_sample.sh" ] ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:in , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "normalized.vcf.gz" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:in , , ; cwl:out ; cwl:run . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:default 0 ; cwl:inputBinding [ CommandLineBinding:position 4 ] ; sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; cwl:inputBinding [ CommandLineBinding:prefix "-t" ] ; sld:type sld:null ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] ; sld:type [ sld:symbols , , ; sld:type sld:enum ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "combined.vcf.gz" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:source . cwl:default "variants" ; sld:type xsd:string , sld:null . cwl:in , , , , , ; cwl:out , ; cwl:run . a cwl:CommandLineTool ; rdfs:label "bgzip VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:arguments ( "-c" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:baseCommand ( "/opt/htslib/bin/bgzip" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:stdout "$(inputs.file.basename).gz" . cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.Germline.vcf" ] ; sld:type cwl:File . sld:type xsd:float . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:valueFrom "strelka" . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--max-normal-freq" ] ; sld:type xsd:float , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . rdfs:comment "ensembl version - Must be present in the cache directory. Example: 95" ; sld:type xsd:string . cwl:source . cwl:source . cwl:source . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.LOH.vcf" ] ; sld:type cwl:File . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type cwl:File . rdfs:label "Force report the overlapping coordinates of custom feature instead of based on the exact coordinates" ; sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "SelectVariants (GATK 3.6)" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/$(inputs.output_vcf_basename).vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "SelectVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "add GT tags" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "/usr/bin/perl" "add_strelka_gt.pl" "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "#!/usr/bin/perl\n\nuse strict;\nuse warnings;\n\nuse feature qw(say);\n\ndie(\"wrong number of arguments\") unless scalar(@ARGV) == 2;\nmy ($strelka_vcf, $outdir) = @ARGV;\n\nopen(my $strelka_vcf_fh, '-|', '/bin/gunzip', '-c', $strelka_vcf) \n or die(\"couldn't open $strelka_vcf to read\");\nopen(my $add_gt_fh, \">\", \"$outdir/add_gt.vcf\") \n or die(\"couldn't open add_gt.vcf for write\");\n\nwhile (<$strelka_vcf_fh>) {\n chomp;\n if (/^##/) {\n say $add_gt_fh $_;\n }\n elsif (/^#/) { #COLUMN HEADER\n say $add_gt_fh '##FORMAT=';\n say $add_gt_fh $_;\n }\n else {\n my @columns = split /\\t/, $_;\n my ($ref, $alt, $info) = map{$columns[$_]}(3, 4, 7);\n my @alts = split /,/, $alt;\n\n my ($n_gt, $t_gt);\n\n if (length($ref) == 1 and length($alts[0]) == 1) {\n my ($n_gt_info, $n_gt_str, $t_gt_str) = $info =~ /NT=(\\S+?);QSS.*SGT=(\\S+?)\\->(\\S+?);/;\n unshift @alts, $ref;\n\n my %ids;\n my $id = 0;\n\n for my $base (@alts) {\n $ids{$base} = $id;\n $id++;\n }\n\n $n_gt = $n_gt_info eq 'ref' ? '0/0' : parse_gt($n_gt_str, \\%ids);\n $t_gt = parse_gt($t_gt_str, \\%ids);\n }\n else {#INDEL\n my ($n_gt_info, $t_gt_info) = $info =~ /;NT=(\\S+?);.*SGT.*\\->(\\S+?);/;\n\n my %gt_info = (\n ref => '0/0',\n het => '0/1',\n hom => '1/1',\n conflict => './.',\n );\n\n $n_gt = $gt_info{$n_gt_info};\n $t_gt = $gt_info{$t_gt_info};\n }\n\n $columns[8] = 'GT:'.$columns[8];\n $columns[9] = $n_gt . ':' . $columns[9];\n $columns[10] = $t_gt . ':' . $columns[10];\n\n my $new_str = join \"\\t\", @columns;\n say $add_gt_fh $new_str;\n }\n}\n\nclose($strelka_vcf_fh);\nclose($add_gt_fh);\n\n\nsub parse_gt {\n my ($gt_str, $ids) = @_;\n my @gt_ids = map{$ids->{$_}}(split //, $gt_str);\n return join '/', sort @gt_ids;\n}\n\n#SNV example\n#1 10231 . C A . QSS_ref NT=ref;QSS=1;QSS_NT=1;SGT=AC->AC;SOMATIC;TQSS=2;TQSS_NT=2 DP:FDP:SDP:SUBDP:AU:CU:GU:TU 32:4:8:0:0,3:28,60:0,0:0,1 84:6:69:0:7,21:71,192:0,0:0,1\n#INDEL example\n##1 965051 . ATGTGTG A . QSI_ref IC=5;IHP=2;NT=ref;QSI=1;QSI_NT=1;RC=8;RU=TG;SGT=het->het;SOMATIC;TQSI=1;TQSI_NT=1 DP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50 8:8:6,6:0,0:2,4:10.3:0.00:0.00 18:18:8,8:5,6:5,8:21:0.25:0.00\n" ; cwl:entryname "add_strelka_gt.pl" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:inputBinding [ CommandLineBinding:position 4 ] ; cwl:secondaryFiles [] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; rdfs:label "add bam_readcount info to vcf" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/annotated.bam_readcount.vcf.gz" ] ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:baseCommand ( "vcf-readcount-annotator" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "griffithlab/vatools:3.1.0" ] . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "HGVSp" , "HGVSc" ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:source . rdfs:label "custom annotation file to be used by vep" ; sld:fields , , ; sld:type sld:record . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -8 ] ; cwl:inputBinding [ CommandLineBinding:position -8 ] ; sld:type cwl:File . cwl:source . sld:type xsd:string , sld:null . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:int , sld:null . sld:type xsd:string . cwl:source , . cwl:source . cwl:source . cwl:default true ; cwl:inputBinding [ CommandLineBinding:position 9 ; CommandLineBinding:prefix "--everything" ] ; sld:type xsd:boolean , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 5 ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out , ; cwl:run . sld:type xsd:string . rdfs:comment "include genotypes from this sample" ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--sample_name" ] ; sld:type sld:null ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:docm" ] ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--vcf-file" ] ; sld:type cwl:File . sld:type xsd:int , sld:null . sld:type xsd:int , sld:null . cwl:source . sld:type xsd:float . sld:type xsd:float , sld:null . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead." ; rdfs:label "Staged Renamer" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.original.basename)" "$(inputs.name)" ) ; cwl:baseCommand ( "/bin/mv" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "ubuntu:bionic" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing "$(inputs.original)" ] . sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "output.vcf.gz" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:prefix "--normal-sample-name" ] ; sld:type xsd:string . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "OUTPUT=$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/usr/bin/perl" "split_interval_list_helper.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "use File::Copy;\n\nmy $retval = system('/usr/bin/java', '-jar', '/usr/picard/picard.jar', 'IntervalListTools', @ARGV);\nexit $retval if $retval != 0;\n\nmy $i = 1;\nfor(glob('*/scattered.interval_list')) {\n #create unique names and relocate all the scattered intervals to a single directory\n File::Copy::move($_, qq{$i.interval_list});\n $i++\n}\n" ; cwl:entryname "split_interval_list_helper.pl" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 6000 ] . cwl:source . cwl:source . cwl:default "TUMOR" ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--sample" ] ; sld:type xsd:string , sld:null . cwl:in , , , ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--variant" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position -3 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Normalize variants" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:arguments ( "-o" [ cwl:valueFrom "$(runtime.outdir)/normalized.vcf.gz" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx8g" "-jar" "/opt/GenomeAnalysisTK.jar" "-T" "LeftAlignAndTrimVariants" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/gatk-cwl:3.6.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 9000 ] . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "SCATTER_COUNT=" ; CommandLineBinding:separate false ] ; sld:type xsd:int . cwl:source . sld:type cwl:File . cwl:source . sld:type xsd:string . cwl:in , , ; cwl:out ; cwl:run . sld:type cwl:File , sld:null . cwl:default "DNA" . cwl:source . cwl:source . sld:type xsd:string . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "$(self.basename)" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; cwl:outputBinding [ CommandOutputBinding:glob "annotated.bam_readcount.vcf.gz" ] ; sld:type cwl:File . a cwl:Workflow ; rdfs:label "bgzip and index VCF" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs . cwl:source . cwl:default "NORMAL" . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:float , sld:null . a cwl:CommandLineTool ; rdfs:label "varscan v2.4.2 processSomatic" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:arguments ( "cp" "$(inputs.variants.path)" "$(runtime.outdir)/$(inputs.variants.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "java" "-jar" "/opt/varscan/VarScan.jar" "processSomatic" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , , , , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] . a cwl:Workflow ; rdfs:label "Apply filters to VCF file" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] . cwl:outputBinding [ CommandOutputBinding:glob "annotated.vcf_summary.html" ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--synonyms" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position -7 ] ; cwl:inputBinding [ CommandLineBinding:position -7 ] ; sld:type xsd:string . cwl:default 9.9e-01 ; cwl:inputBinding [ CommandLineBinding:position 7 ] ; sld:type xsd:float , sld:null . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . cwl:source . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:itemSeparator "," ; CommandLineBinding:position -1 ] ; sld:type [ sld:items xsd:string ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 4 ; CommandLineBinding:prefix "--dir" ] ; sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:in , , , , , , , , , , ; cwl:out , ; cwl:run . sld:type xsd:boolean . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "-L" ] ; sld:type cwl:File , sld:null . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type cwl:File . rdfs:label "Identify known variants colocated with input variant" ; sld:type xsd:boolean . cwl:default 1e-01 ; sld:type xsd:float , sld:null . cwl:source . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . sld:type sld:null ; sld:type [ sld:symbols , , , , , , ; sld:type sld:enum ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:CommandLineTool ; rdfs:label "Sanitize a VCF" ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:baseCommand ( "/bin/bash" "sanitize.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\n# 1) removes lines containing non ACTGN bases, as they conflict with the VCF spec\n# and cause GATK to choke\n# 2) removes mutect-specific format tags containing underscores, which are likewise\n# illegal in the vcf spec\nbase=`basename $1`\noutbase=`echo $base | perl -pe 's/.vcf(.gz)?$//g'`\necho \"$1 $base $outbase\"\nif [[ \"$1\" =~ \".gz\" ]];then\n #gzipped input\n gunzip -c \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nelse\n #non-gzipped input\n cat \"$1\" | perl -a -F'\\t' -ne 'print $_ if $_ =~ /^#/ || $F[3] !~ /[^ACTGNactgn]/' | sed -e \"s/ALT_F1R2/ALTF1R2/g;s/ALT_F2R1/ALTF2R1/g;s/REF_F1R2/REFF1R2/g;s/REF_F2R1/REFF2R1/g\" >$outbase.sanitized.vcf\nfi\n/opt/htslib/bin/bgzip $outbase.sanitized.vcf\n/usr/bin/tabix -p vcf $outbase.sanitized.vcf.gz\n" ; cwl:entryname "sanitize.sh" ] ] . cwl:inputBinding [ CommandLineBinding:position -2 ; CommandLineBinding:prefix "--llr-threshold" ] ; sld:type xsd:float . cwl:source . a cwl:CommandLineTool ; rdfs:label "cle_annotated_vcf_filter" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(inputs.vcf.path)" "$(runtime.outdir)" ) ; cwl:baseCommand ( "/usr/bin/perl" "/usr/bin/docm_and_coding_indel_selection.pl" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/cle:v1.3.1" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . sld:type xsd:int , sld:null . cwl:default "TUMOR" . cwl:in , ; cwl:out , , , , , ; cwl:run . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 8 ] ; sld:type cwl:File , sld:null . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--variant:varscan" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:default "TUMOR" . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "depth_filtered.vcf" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-R" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File , xsd:string . cwl:source . cwl:source . cwl:default true ; sld:type xsd:boolean , sld:null . cwl:default 8 ; sld:type xsd:int , sld:null . sld:type xsd:boolean . a cwl:CommandLineTool ; rdfs:label "vcf index" ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:arguments ( "cp" "$(inputs.vcf.path)" "$(runtime.outdir)/$(inputs.vcf.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/usr/bin/tabix" "-p" "vcf" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . a cwl:Workflow ; rdfs:label "fp_filter workflow" ; ns1:original_cwlVersion "v1.2" ; Workflow:steps , , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if(inputs.filter_docm_variants){\n return \"1\";\n } else {\n return \"0\";\n }\n}\n" ] ; sld:type xsd:boolean . cwl:in , , ; cwl:out ; cwl:run . cwl:source .