{"@id":"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","retrievedFrom":{"repoUrl":"https://github.com/hubmapconsortium/salmon-rnaseq.git","branch":"81e4484986251c48e3edbf5e1f141ab68677b8bd","path":"steps/salmon-quantification.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/hubmapconsortium/salmon-rnaseq/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","url":"https://github.com/hubmapconsortium/salmon-rnaseq/blob/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl"},"retrievedOn":"2026-09-26T23:53:03.918+00:00","lastCommit":"81e4484986251c48e3edbf5e1f141ab68677b8bd","label":"Salmon quantification, FASTQ -> H5AD count matrix","inputs":{"assay":{"label":"scRNA-seq assay","type":"String"},"img_dir":{"type":"Directory (Optional)"},"threads":{"label":"Number of threads for Salmon","type":"Integer"},"organism":{"type":"String (Optional)"},"fastq_dir":{"label":"Directory containing FASTQ files","type":"Directory[]"},"barcode_file":{"type":"File (Optional)"},"metadata_dir":{"type":"Directory (Optional)"},"keep_all_barcodes":{"type":"Boolean (Optional)"},"expected_cell_count":{"type":"Integer (Optional)"}},"outputs":{"salmon_output":{"label":"Full output of `salmon alevin`","type":"Directory"},"raw_count_matrix":{"label":"Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns","type":"File (Optional)"},"count_matrix_h5ad":{"label":"Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts","type":"File"},"genome_build_json":{"label":"Genome build information in JSON format","type":"File"}},"steps":{"salmon":{"label":"Run Salmon Alevin tool on FASTQ input","run":"salmon-quantification/salmon.cwl","runType":"COMMANDLINETOOL","sources":{"salmon":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/assay":{"sourceIDs":["assay"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/organism":{"sourceIDs":["organism"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/barcode_file":{"sourceIDs":["barcode_file"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/orig_fastq_dirs":{"sourceIDs":["fastq_dir"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/keep_all_barcodes":{"sourceIDs":["keep_all_barcodes"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/trimmed_fastq_dir":{"sourceIDs":["trim_reads"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon/expected_cell_count":{"sourceIDs":["expected_cell_count"]}}},"trim_reads":{"label":"Trim FASTQ files","run":"salmon-quantification/trim-reads.cwl","runType":"COMMANDLINETOOL","sources":{"trim_reads":{"sourceIDs":["adjust_barcodes"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/assay":{"sourceIDs":["assay"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#trim_reads/orig_fastq_dirs":{"sourceIDs":["fastq_dir"]}}},"salmon-mouse":{"label":"Run Salmon Alevin tool on FASTQ input","run":"salmon-quantification/salmon-mouse.cwl","runType":"COMMANDLINETOOL","sources":{"salmon-mouse":{"sourceIDs":["organism"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/assay":{"sourceIDs":["assay"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/barcode_file":{"sourceIDs":["barcode_file"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/orig_fastq_dirs":{"sourceIDs":["fastq_dir"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/keep_all_barcodes":{"sourceIDs":["keep_all_barcodes"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/trimmed_fastq_dir":{"sourceIDs":["trim_reads"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#salmon-mouse/expected_cell_count":{"sourceIDs":["expected_cell_count"]}}},"annotate_cells":{"label":"Assay-specific annotation of cell barcodes after quantification","run":"salmon-quantification/annotate-cells.cwl","runType":"COMMANDLINETOOL","sources":{"annotate_cells":{"sourceIDs":["img_dir"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/assay":{"sourceIDs":["assay"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/h5ad_file":{"sourceIDs":["alevin_to_anndata"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_dir":{"sourceIDs":["metadata_dir"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/metadata_json":{"sourceIDs":["adjust_barcodes"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#annotate_cells/orig_fastq_dirs":{"sourceIDs":["fastq_dir"]}}},"adjust_barcodes":{"label":"Assay-specific adjustment of cell barcodes","run":"salmon-quantification/adjust-barcodes.cwl","runType":"COMMANDLINETOOL","sources":{"adjust_barcodes":{"sourceIDs":["fastq_dir"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#adjust_barcodes/assay":{"sourceIDs":["assay"]}}},"alevin_to_anndata":{"label":"Convert Alevin sparse output to anndata.AnnData object, save as h5ad","run":"salmon-quantification/alevin-to-anndata.cwl","runType":"COMMANDLINETOOL","sources":{"alevin_to_anndata":{"sourceIDs":["organism"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/assay":{"sourceIDs":["assay"]},"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl#alevin_to_anndata/alevin_dir":{"sourceIDs":["salmon-mouse"]}}}},"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    \"img_dir\" [fillcolor=\"#94DDF4\",label=\"img_dir\"];\n    \"threads\" [fillcolor=\"#94DDF4\",label=\"Number of threads for Salmon\"];\n    \"metadata_dir\" [fillcolor=\"#94DDF4\",label=\"metadata_dir\"];\n    \"organism\" [fillcolor=\"#94DDF4\",label=\"organism\"];\n    \"fastq_dir\" [fillcolor=\"#94DDF4\",label=\"Directory containing FASTQ files\"];\n    \"expected_cell_count\" [fillcolor=\"#94DDF4\",label=\"expected_cell_count\"];\n    \"assay\" [fillcolor=\"#94DDF4\",label=\"scRNA-seq assay\"];\n    \"barcode_file\" [fillcolor=\"#94DDF4\",label=\"barcode_file\"];\n    \"keep_all_barcodes\" [fillcolor=\"#94DDF4\",label=\"keep_all_barcodes\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"raw_count_matrix\" [fillcolor=\"#94DDF4\",label=\"Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns\"];\n    \"salmon_output\" [fillcolor=\"#94DDF4\",label=\"Full output of `salmon alevin`\"];\n    \"genome_build_json\" [fillcolor=\"#94DDF4\",label=\"Genome build information in JSON format\"];\n    \"count_matrix_h5ad\" [fillcolor=\"#94DDF4\",label=\"Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts\"];\n  }\n  \"alevin_to_anndata\" [label=\"Convert Alevin sparse output to anndata.AnnData object, save as h5ad\"];\n  \"adjust_barcodes\" [label=\"Assay-specific adjustment of cell barcodes\"];\n  \"salmon\" [label=\"Run Salmon Alevin tool on FASTQ input\"];\n  \"annotate_cells\" [label=\"Assay-specific annotation of cell barcodes after quantification\"];\n  \"trim_reads\" [label=\"Trim FASTQ files\"];\n  \"salmon-mouse\" [label=\"Run Salmon Alevin tool on FASTQ input\"];\n  \"organism\" -> \"alevin_to_anndata\" [label=\"organism\"];\n  \"assay\" -> \"alevin_to_anndata\" [label=\"assay\"];\n  \"salmon\" -> \"alevin_to_anndata\" [label=\"alevin_dir\"];\n  \"salmon-mouse\" -> \"alevin_to_anndata\" [label=\"alevin_dir\"];\n  \"fastq_dir\" -> \"adjust_barcodes\" [label=\"fastq_dir\"];\n  \"assay\" -> \"adjust_barcodes\" [label=\"assay\"];\n  \"threads\" -> \"salmon\" [label=\"threads\"];\n  \"trim_reads\" -> \"salmon\" [label=\"trimmed_fastq_dir\"];\n  \"barcode_file\" -> \"salmon\" [label=\"barcode_file\"];\n  \"keep_all_barcodes\" -> \"salmon\" [label=\"keep_all_barcodes\"];\n  \"assay\" -> \"salmon\" [label=\"assay\"];\n  \"organism\" -> \"salmon\" [label=\"organism\"];\n  \"fastq_dir\" -> \"salmon\" [label=\"orig_fastq_dirs\"];\n  \"expected_cell_count\" -> \"salmon\" [label=\"expected_cell_count\"];\n  \"img_dir\" -> \"annotate_cells\" [label=\"img_dir\"];\n  \"fastq_dir\" -> \"annotate_cells\" [label=\"orig_fastq_dirs\"];\n  \"adjust_barcodes\" -> \"annotate_cells\" [label=\"metadata_json\"];\n  \"metadata_dir\" -> \"annotate_cells\" [label=\"metadata_dir\"];\n  \"alevin_to_anndata\" -> \"annotate_cells\" [label=\"h5ad_file\"];\n  \"assay\" -> \"annotate_cells\" [label=\"assay\"];\n  \"adjust_barcodes\" -> \"trim_reads\" [label=\"adj_fastq_dir\"];\n  \"fastq_dir\" -> \"trim_reads\" [label=\"orig_fastq_dirs\"];\n  \"threads\" -> \"trim_reads\" [label=\"threads\"];\n  \"assay\" -> \"trim_reads\" [label=\"assay\"];\n  \"organism\" -> \"salmon-mouse\" [label=\"organism\"];\n  \"barcode_file\" -> \"salmon-mouse\" [label=\"barcode_file\"];\n  \"threads\" -> \"salmon-mouse\" [label=\"threads\"];\n  \"trim_reads\" -> \"salmon-mouse\" [label=\"trimmed_fastq_dir\"];\n  \"expected_cell_count\" -> \"salmon-mouse\" [label=\"expected_cell_count\"];\n  \"keep_all_barcodes\" -> \"salmon-mouse\" [label=\"keep_all_barcodes\"];\n  \"assay\" -> \"salmon-mouse\" [label=\"assay\"];\n  \"fastq_dir\" -> \"salmon-mouse\" [label=\"orig_fastq_dirs\"];\n  \"alevin_to_anndata\" -> \"raw_count_matrix\";\n  \"salmon\" -> \"salmon_output\";\n  \"salmon-mouse\" -> \"salmon_output\";\n  \"alevin_to_anndata\" -> \"genome_build_json\";\n  \"annotate_cells\" -> \"count_matrix_h5ad\";\n}\n","licenseLink":"https://spdx.org/licenses/GPL-3.0","permalink":"https://w3id.org/cwl/view/git/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/hubmapconsortium/salmon-rnaseq/blob/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","visualisationPng":"/graph/png/github.com/hubmapconsortium/salmon-rnaseq/blob/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","visualisationSvg":"/graph/svg/github.com/hubmapconsortium/salmon-rnaseq/blob/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","roBundle":"/robundle/github.com/hubmapconsortium/salmon-rnaseq/blob/81e4484986251c48e3edbf5e1f141ab68677b8bd/steps/salmon-quantification.cwl","licenseName":"GNU General Public License v3.0 only"}