{"@id":"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/cancer-genomics-workflow.git","branch":"ee1afbcbe01fd17715b54d23e556a23086aeec57","path":"qc/workflow_wgs.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/cancer-genomics-workflow/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","url":"https://github.com/genome/cancer-genomics-workflow/blob/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl"},"retrievedOn":"2026-08-28T19:11:15.687+00:00","lastCommit":"ee1afbcbe01fd17715b54d23e556a23086aeec57","label":"WGS QC workflow","inputs":{"cram":{"type":"File"},"omni_vcf":{"type":"File"},"intervals":{"type":"File"},"reference":{"type":"String"},"picard_metric_accumulation_level":{"type":"String (Optional)"}},"outputs":{"flagstats":{"type":"File"},"wgs_metrics":{"type":"File"},"gc_bias_metrics":{"type":"File"},"insert_size_metrics":{"type":"File"},"verify_bam_id_depth":{"type":"File"},"gc_bias_metrics_chart":{"type":"File"},"verify_bam_id_metrics":{"type":"File"},"gc_bias_metrics_summary":{"type":"File"},"alignment_summary_metrics":{"type":"File"}},"steps":{"cram_to_bam":{"label":"cram_to_bam workflow","run":"../cram_to_bam/workflow.cwl","runType":"WORKFLOW","sources":{"cram_to_bam":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#cram_to_bam/cram":{"sourceIDs":["cram"]}}},"verify_bam_id":{"label":"verify BAM ID","run":"verify_bam_id.cwl","runType":"COMMANDLINETOOL","sources":{"verify_bam_id":{"sourceIDs":["omni_vcf"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#verify_bam_id/bam":{"sourceIDs":["cram_to_bam"]}}},"samtools_flagstat":{"label":"samtools flagstat","run":"samtools_flagstat.cwl","runType":"COMMANDLINETOOL","sources":{"samtools_flagstat":{"sourceIDs":["cram"]}}},"collect_wgs_metrics":{"label":"collect WGS metrics","run":"collect_wgs_metrics.cwl","runType":"COMMANDLINETOOL","sources":{"collect_wgs_metrics":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/cram":{"sourceIDs":["cram"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_wgs_metrics/intervals":{"sourceIDs":["intervals"]}}},"collect_gc_bias_metrics":{"label":"collect gc bias metrics","run":"collect_gc_bias_metrics.cwl","runType":"COMMANDLINETOOL","sources":{"collect_gc_bias_metrics":{"sourceIDs":["cram"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_gc_bias_metrics/metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]}}},"collect_insert_size_metrics":{"label":"collect insert size metrics","run":"collect_insert_size_metrics.cwl","runType":"COMMANDLINETOOL","sources":{"collect_insert_size_metrics":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/cram":{"sourceIDs":["cram"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_insert_size_metrics/metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]}}},"collect_alignment_summary_metrics":{"label":"collect alignment summary metrics","run":"collect_alignment_summary_metrics.cwl","runType":"COMMANDLINETOOL","sources":{"collect_alignment_summary_metrics":{"sourceIDs":["picard_metric_accumulation_level"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/cram":{"sourceIDs":["cram"]},"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl#collect_alignment_summary_metrics/reference":{"sourceIDs":["reference"]}}}},"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    \"intervals\" [fillcolor=\"#94DDF4\",label=\"intervals\"];\n    \"omni_vcf\" [fillcolor=\"#94DDF4\",label=\"omni_vcf\"];\n    \"cram\" [fillcolor=\"#94DDF4\",label=\"cram\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\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    \"verify_bam_id_depth\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_depth\"];\n    \"gc_bias_metrics_summary\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_summary\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"verify_bam_id_metrics\" [fillcolor=\"#94DDF4\",label=\"verify_bam_id_metrics\"];\n    \"wgs_metrics\" [fillcolor=\"#94DDF4\",label=\"wgs_metrics\"];\n    \"gc_bias_metrics_chart\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_chart\"];\n    \"gc_bias_metrics\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n  }\n  \"cram_to_bam\" [label=\"cram_to_bam workflow\", fillcolor=\"#F3CEA1\"];\n  \"samtools_flagstat\" [label=\"samtools flagstat\"];\n  \"collect_alignment_summary_metrics\" [label=\"collect alignment summary metrics\"];\n  \"collect_wgs_metrics\" [label=\"collect WGS metrics\"];\n  \"collect_gc_bias_metrics\" [label=\"collect gc bias metrics\"];\n  \"verify_bam_id\" [label=\"verify BAM ID\"];\n  \"collect_insert_size_metrics\" [label=\"collect insert size metrics\"];\n  \"reference\" -> \"cram_to_bam\" [label=\"reference\"];\n  \"cram\" -> \"cram_to_bam\" [label=\"cram\"];\n  \"cram\" -> \"samtools_flagstat\" [label=\"cram\"];\n  \"picard_metric_accumulation_level\" -> \"collect_alignment_summary_metrics\" [label=\"metric_accumulation_level\"];\n  \"reference\" -> \"collect_alignment_summary_metrics\" [label=\"reference\"];\n  \"cram\" -> \"collect_alignment_summary_metrics\" [label=\"cram\"];\n  \"reference\" -> \"collect_wgs_metrics\" [label=\"reference\"];\n  \"cram\" -> \"collect_wgs_metrics\" [label=\"cram\"];\n  \"intervals\" -> \"collect_wgs_metrics\" [label=\"intervals\"];\n  \"cram\" -> \"collect_gc_bias_metrics\" [label=\"cram\"];\n  \"picard_metric_accumulation_level\" -> \"collect_gc_bias_metrics\" [label=\"metric_accumulation_level\"];\n  \"reference\" -> \"collect_gc_bias_metrics\" [label=\"reference\"];\n  \"omni_vcf\" -> \"verify_bam_id\" [label=\"vcf\"];\n  \"cram_to_bam\" -> \"verify_bam_id\" [label=\"bam\"];\n  \"reference\" -> \"collect_insert_size_metrics\" [label=\"reference\"];\n  \"picard_metric_accumulation_level\" -> \"collect_insert_size_metrics\" [label=\"metric_accumulation_level\"];\n  \"cram\" -> \"collect_insert_size_metrics\" [label=\"cram\"];\n  \"verify_bam_id\" -> \"verify_bam_id_depth\";\n  \"collect_gc_bias_metrics\" -> \"gc_bias_metrics_summary\";\n  \"collect_insert_size_metrics\" -> \"insert_size_metrics\";\n  \"samtools_flagstat\" -> \"flagstats\";\n  \"verify_bam_id\" -> \"verify_bam_id_metrics\";\n  \"collect_wgs_metrics\" -> \"wgs_metrics\";\n  \"collect_gc_bias_metrics\" -> \"gc_bias_metrics_chart\";\n  \"collect_gc_bias_metrics\" -> \"gc_bias_metrics\";\n  \"collect_alignment_summary_metrics\" -> \"alignment_summary_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/cancer-genomics-workflow/blob/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","visualisationPng":"/graph/png/github.com/genome/cancer-genomics-workflow/blob/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","visualisationSvg":"/graph/svg/github.com/genome/cancer-genomics-workflow/blob/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","roBundle":"/robundle/github.com/genome/cancer-genomics-workflow/blob/ee1afbcbe01fd17715b54d23e556a23086aeec57/qc/workflow_wgs.cwl","licenseName":"MIT License"}