{"@id":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","retrievedFrom":{"repoUrl":"https://github.com/genome/analysis-workflows.git","branch":"1585504ccffafac53b1594349ed934f45206ee2b","path":"definitions/pipelines/chipseq_alignment_mouse.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/genome/analysis-workflows/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","url":"https://github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl"},"retrievedOn":"2026-09-14T00:38:05.871+00:00","lastCommit":"1585504ccffafac53b1594349ed934f45206ee2b","label":"Chipseq alignment for mouse with qc and creating homer tag directory","inputs":{"reference":{"type":"String"},"final_name":{"type":"String (Optional)"},"chipseq_sequence":{"type":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/types/sequence_data.yml#sequence_data[]"},"summary_intervals":{"type":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/types/labelled_file.yml#labelled_file[] (Optional)"},"per_base_intervals":{"type":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/types/labelled_file.yml#labelled_file[] (Optional)"},"minimum_base_quality":{"type":"Integer (Optional)"},"per_target_intervals":{"type":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/types/labelled_file.yml#labelled_file[] (Optional)"},"minimum_mapping_quality":{"type":"Integer (Optional)"},"picard_metric_accumulation_level":{"type":"String"}},"outputs":{"bam":{"type":"File"},"flagstats":{"type":"File"},"wgs_metrics":{"type":"File"},"tag_directory":{"type":"Directory"},"gc_bias_metrics":{"type":"File"},"bamcoverage_bigwig":{"type":"File"},"summary_hs_metrics":{"type":"File[]"},"insert_size_metrics":{"type":"File"},"per_base_hs_metrics":{"type":"File[]"},"gc_bias_metrics_chart":{"type":"File"},"insert_size_histogram":{"type":"File"},"per_target_hs_metrics":{"type":"File[]"},"gc_bias_metrics_summary":{"type":"File"},"mark_duplicates_metrics":{"type":"File"},"alignment_summary_metrics":{"type":"File"},"per_base_coverage_metrics":{"type":"File[]"},"per_target_coverage_metrics":{"type":"File[]"}},"steps":{"qc":{"label":"WGS QC workflow mouse","run":"../subworkflows/qc_wgs_mouse.cwl","runType":"WORKFLOW","sources":{"qc":{"sourceIDs":["summary_intervals"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/bam":{"sourceIDs":["alignment"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/per_base_intervals":{"sourceIDs":["per_base_intervals"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/minimum_base_quality":{"sourceIDs":["minimum_base_quality"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/per_target_intervals":{"sourceIDs":["per_target_intervals"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/minimum_mapping_quality":{"sourceIDs":["minimum_mapping_quality"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#qc/picard_metric_accumulation_level":{"sourceIDs":["picard_metric_accumulation_level"]}}},"alignment":{"label":"Aligning chipseq data of mouse","run":"../subworkflows/sequence_to_bqsr_mouse.cwl","runType":"WORKFLOW","sources":{"alignment":{"sourceIDs":["chipseq_sequence"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#alignment/reference":{"sourceIDs":["reference"]},"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl#alignment/final_name":{"sourceIDs":["final_name"]}}},"bam_to_sam":{"label":"BAM to SAM conversion","run":"../tools/bam_to_sam.cwl","runType":"COMMANDLINETOOL","sources":{"bam_to_sam":{"sourceIDs":["alignment"]}}},"homer_tag_directory":{"label":"Creating the homer tag directory","run":"../tools/homer_tag_directory.cwl","runType":"COMMANDLINETOOL","sources":{"homer_tag_directory":{"sourceIDs":["bam_to_sam"]}}}},"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    \"summary_intervals\" [fillcolor=\"#94DDF4\",label=\"summary_intervals\"];\n    \"minimum_mapping_quality\" [fillcolor=\"#94DDF4\",label=\"minimum_mapping_quality\"];\n    \"chipseq_sequence\" [fillcolor=\"#94DDF4\",label=\"chipseq_sequence\"];\n    \"per_base_intervals\" [fillcolor=\"#94DDF4\",label=\"per_base_intervals\"];\n    \"final_name\" [fillcolor=\"#94DDF4\",label=\"final_name\"];\n    \"reference\" [fillcolor=\"#94DDF4\",label=\"reference\"];\n    \"minimum_base_quality\" [fillcolor=\"#94DDF4\",label=\"minimum_base_quality\"];\n    \"per_target_intervals\" [fillcolor=\"#94DDF4\",label=\"per_target_intervals\"];\n    \"picard_metric_accumulation_level\" [fillcolor=\"#94DDF4\",label=\"picard_metric_accumulation_level\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"per_base_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_hs_metrics\"];\n    \"insert_size_metrics\" [fillcolor=\"#94DDF4\",label=\"insert_size_metrics\"];\n    \"wgs_metrics\" [fillcolor=\"#94DDF4\",label=\"wgs_metrics\"];\n    \"summary_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"summary_hs_metrics\"];\n    \"gc_bias_metrics\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics\"];\n    \"bamcoverage_bigwig\" [fillcolor=\"#94DDF4\",label=\"bamcoverage_bigwig\"];\n    \"per_base_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_base_coverage_metrics\"];\n    \"gc_bias_metrics_summary\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_summary\"];\n    \"flagstats\" [fillcolor=\"#94DDF4\",label=\"flagstats\"];\n    \"per_target_hs_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_hs_metrics\"];\n    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n    \"gc_bias_metrics_chart\" [fillcolor=\"#94DDF4\",label=\"gc_bias_metrics_chart\"];\n    \"tag_directory\" [fillcolor=\"#94DDF4\",label=\"tag_directory\"];\n    \"insert_size_histogram\" [fillcolor=\"#94DDF4\",label=\"insert_size_histogram\"];\n    \"alignment_summary_metrics\" [fillcolor=\"#94DDF4\",label=\"alignment_summary_metrics\"];\n    \"per_target_coverage_metrics\" [fillcolor=\"#94DDF4\",label=\"per_target_coverage_metrics\"];\n    \"mark_duplicates_metrics\" [fillcolor=\"#94DDF4\",label=\"mark_duplicates_metrics\"];\n  }\n  \"bam_to_sam\" [label=\"BAM to SAM conversion\"];\n  \"homer_tag_directory\" [label=\"Creating the homer tag directory\"];\n  \"alignment\" [label=\"Aligning chipseq data of mouse\", fillcolor=\"#F3CEA1\"];\n  \"qc\" [label=\"WGS QC workflow mouse\", fillcolor=\"#F3CEA1\"];\n  \"alignment\" -> \"bam_to_sam\" [label=\"bam\"];\n  \"bam_to_sam\" -> \"homer_tag_directory\" [label=\"sam\"];\n  \"chipseq_sequence\" -> \"alignment\" [label=\"unaligned\"];\n  \"final_name\" -> \"alignment\" [label=\"final_name\"];\n  \"reference\" -> \"alignment\" [label=\"reference\"];\n  \"summary_intervals\" -> \"qc\" [label=\"summary_intervals\"];\n  \"minimum_mapping_quality\" -> \"qc\" [label=\"minimum_mapping_quality\"];\n  \"alignment\" -> \"qc\" [label=\"bam\"];\n  \"picard_metric_accumulation_level\" -> \"qc\" [label=\"picard_metric_accumulation_level\"];\n  \"reference\" -> \"qc\" [label=\"reference\"];\n  \"minimum_base_quality\" -> \"qc\" [label=\"minimum_base_quality\"];\n  \"per_base_intervals\" -> \"qc\" [label=\"per_base_intervals\"];\n  \"per_target_intervals\" -> \"qc\" [label=\"per_target_intervals\"];\n  \"qc\" -> \"per_base_hs_metrics\";\n  \"qc\" -> \"insert_size_metrics\";\n  \"qc\" -> \"wgs_metrics\";\n  \"qc\" -> \"summary_hs_metrics\";\n  \"qc\" -> \"gc_bias_metrics\";\n  \"qc\" -> \"bamcoverage_bigwig\";\n  \"qc\" -> \"per_base_coverage_metrics\";\n  \"qc\" -> \"gc_bias_metrics_summary\";\n  \"qc\" -> \"flagstats\";\n  \"qc\" -> \"per_target_hs_metrics\";\n  \"alignment\" -> \"bam\";\n  \"qc\" -> \"gc_bias_metrics_chart\";\n  \"homer_tag_directory\" -> \"tag_directory\";\n  \"qc\" -> \"insert_size_histogram\";\n  \"qc\" -> \"alignment_summary_metrics\";\n  \"qc\" -> \"per_target_coverage_metrics\";\n  \"alignment\" -> \"mark_duplicates_metrics\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","visualisationPng":"/graph/png/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","visualisationSvg":"/graph/svg/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","roBundle":"/robundle/github.com/genome/analysis-workflows/blob/1585504ccffafac53b1594349ed934f45206ee2b/definitions/pipelines/chipseq_alignment_mouse.cwl","licenseName":"MIT License"}