{"@id":"https://w3id.org/cwl/view/git/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl","retrievedFrom":{"repoUrl":"https://github.com/common-workflow-library/bio-cwl-tools.git","branch":"810495363e06f80529633389ec25f8bb6b961844","path":"bwa/BWA-Mem2-single.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/common-workflow-library/bio-cwl-tools/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl","url":"https://github.com/common-workflow-library/bio-cwl-tools/blob/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl"},"retrievedOn":"2025-04-24T22:39:53.324+00:00","lastCommit":"810495363e06f80529633389ec25f8bb6b961844","label":"map medium and long reads (> 100 bp) against reference genome\n","inputs":{"reads":{"label":"Sequences to map to the reference genome.","type":"File [FASTQ-sanger]","format":"http://edamontology.org/format_1932"},"sort_mode":{"label":"How to sort the alignments, if at all","doc":"* coordinate: Sort by chromosomal coordinates\n* name: Sort by read names  (i.e., the QNAME field)\n* unsorted: Not sorted (sorted as input)\n"},"read_group":{"label":"Specify read group details manually.","type":"https://w3id.org/cwl/view/git/810495363e06f80529633389ec25f8bb6b961844/bwa/ReadGroupType.yml#ReadGroupDetails (Optional)"},"do_auto_name":{"label":"Auto-assign read groups","doc":"If true, use the file name to automatically assign the read groups value.","type":"Boolean"},"reference_genome":{"label":"Reference genome sequences, optionally already indexed for BWA-Mem2.","type":"File [FASTA]","format":"http://edamontology.org/format_1929"}},"outputs":{"alignments":{"label":"Alignments of the reads to the references genome","type":"File [BAM]","format":"http://edamontology.org/format_2572"}},"steps":{"sort":{"doc":"Sort a bam file by read names.","run":"../samtools/samtools_sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort":{"sourceIDs":["align"]},"https://w3id.org/cwl/view/git/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl#sort/by_name":{"sourceIDs":["sort_mode"]},"https://w3id.org/cwl/view/git/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl#sort/sort_mode":{"sourceIDs":["sort_mode"]}}},"align":{"label":"map medium and long reads (> 100 bp) against reference 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SAM to BAM.\n","run":"../samtools/samtools_view_sam2bam.cwl","runType":"COMMANDLINETOOL","sources":{"convert_unsorted_alignments_to_bam":{"sourceIDs":["align"]},"https://w3id.org/cwl/view/git/810495363e06f80529633389ec25f8bb6b961844/bwa/BWA-Mem2-single.cwl#convert_unsorted_alignments_to_bam/sort_mode":{"sourceIDs":["sort_mode"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph 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