{"@id":"https://w3id.org/cwl/view/git/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/griffithlab/pmbio.org.git","branch":"2752fced5318c012da26546203329e8aa2e2d436","path":"assets/CWL/workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/griffithlab/pmbio.org/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","url":"https://github.com/griffithlab/pmbio.org/blob/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl"},"retrievedOn":"2026-10-27T03:40:59.713+00:00","lastCommit":"2752fced5318c012da26546203329e8aa2e2d436","label":"alignment workflow","inputs":{"bam":{"doc":"bam file to align","type":"File"},"reference":{"doc":"gzipped reference fasta to align to","type":"File"}},"outputs":{"bam_index_out":{"type":"File"},"index_ref_out":{"type":"File"}},"steps":{"sam2bam":{"run":"sam2bam.cwl","runType":"COMMANDLINETOOL","sources":{"sam2bam":{"sourceIDs":["align_fastq"]}}},"sort_bam":{"run":"sort_bam.cwl","runType":"COMMANDLINETOOL","sources":{"sort_bam":{"sourceIDs":["sam2bam"]}}},"bwa_index":{"run":"bwa_index.cwl","runType":"COMMANDLINETOOL","sources":{"bwa_index":{"sourceIDs":["gnu_unzip"]}}},"gnu_unzip":{"run":"gunzip.cwl","runType":"COMMANDLINETOOL","sources":{"gnu_unzip":{"sourceIDs":["reference"]}}},"index_bam":{"run":"bam_index.cwl","runType":"COMMANDLINETOOL","sources":{"index_bam":{"sourceIDs":["sort_bam"]}}},"index_ref":{"run":"index_fa.cwl","runType":"COMMANDLINETOOL","sources":{"index_ref":{"sourceIDs":["gnu_unzip"]}}},"sam2fastq":{"run":"sam2fastq.cwl","runType":"COMMANDLINETOOL","sources":{"sam2fastq":{"sourceIDs":["bam"]}}},"align_fastq":{"run":"bwa_mem.cwl","runType":"COMMANDLINETOOL","sources":{"align_fastq":{"sourceIDs":["bwa_index"]},"https://w3id.org/cwl/view/git/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl#align_fastq/fastq1_file":{"sourceIDs":["sam2fastq"]},"https://w3id.org/cwl/view/git/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl#align_fastq/fastq2_file":{"sourceIDs":["sam2fastq"]}}}},"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 cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"bam_index_out\" [fillcolor=\"#94DDF4\",label=\"bam_index_out\"];\n    \"index_ref_out\" [fillcolor=\"#94DDF4\",label=\"index_ref_out\"];\n  }\n  \"align_fastq\" [label=\"align_fastq\"];\n  \"sam2fastq\" [label=\"sam2fastq\"];\n  \"sam2bam\" [label=\"sam2bam\"];\n  \"index_ref\" [label=\"index_ref\"];\n  \"index_bam\" [label=\"index_bam\"];\n  \"gnu_unzip\" [label=\"gnu_unzip\"];\n  \"bwa_index\" [label=\"bwa_index\"];\n  \"sort_bam\" [label=\"sort_bam\"];\n  \"bwa_index\" -> \"align_fastq\" [label=\"reference_index\"];\n  \"sam2fastq\" -> \"align_fastq\" [label=\"fastq2_file\"];\n  \"sam2fastq\" -> \"align_fastq\" [label=\"fastq1_file\"];\n  \"bam\" -> \"sam2fastq\" [label=\"bam_file\"];\n  \"align_fastq\" -> \"sam2bam\" [label=\"sam_file\"];\n  \"gnu_unzip\" -> \"index_ref\" [label=\"reference_file\"];\n  \"sort_bam\" -> \"index_bam\" [label=\"bam_file\"];\n  \"reference\" -> \"gnu_unzip\" [label=\"reference_file\"];\n  \"gnu_unzip\" -> \"bwa_index\" [label=\"reference_file\"];\n  \"sam2bam\" -> \"sort_bam\" [label=\"bam_file\"];\n  \"index_bam\" -> \"bam_index_out\";\n  \"index_ref\" -> \"index_ref_out\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/griffithlab/pmbio.org/blob/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","visualisationPng":"/graph/png/github.com/griffithlab/pmbio.org/blob/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","visualisationSvg":"/graph/svg/github.com/griffithlab/pmbio.org/blob/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","roBundle":"/robundle/github.com/griffithlab/pmbio.org/blob/2752fced5318c012da26546203329e8aa2e2d436/assets/CWL/workflow.cwl","licenseName":"MIT License"}