{"@id":"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","retrievedFrom":{"repoUrl":"https://github.com/Barski-lab/workflows.git","branch":"744117c1332359de1ed0d2c3c4f314ffcb6797d3","path":"subworkflows/xenbase-sra-to-fastq-pe.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/Barski-lab/workflows/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","url":"https://github.com/Barski-lab/workflows/blob/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl"},"retrievedOn":"2026-10-19T14:36:36.743+00:00","lastCommit":"744117c1332359de1ed0d2c3c4f314ffcb6797d3","label":"xenbase-sra-to-fastq-pe.cwl","inputs":{"threads":{"type":"Integer (Optional)"},"sra_input_file":{"type":"File"},"illumina_adapters_file":{"type":"File"}},"outputs":{"upstream_fastq":{"type":"File"},"downstream_fastq":{"type":"File"}},"steps":{"fastqc_1":{"doc":"Tool runs FastQC from Babraham Bioinformatics\n","run":"../tools/fastqc.cwl","runType":"COMMANDLINETOOL","sources":{"fastqc_1":{"sourceIDs":["sra_to_fastq"]}}},"fastqc_2":{"doc":"Tool runs FastQC from Babraham Bioinformatics\n","run":"../tools/fastqc.cwl","runType":"COMMANDLINETOOL","sources":{"fastqc_2":{"sourceIDs":["sra_to_fastq"]}}},"trimmomatic":{"doc":"Tool runs trimmomatic with ILLUMINACLIP step by default.\n\n`-basein` and `-baseout` inputs are skipped.\n\nIf set `lib_type` to `PE`, both of the inputs `fastq_file_upstream` and `fastq_file_downstream` shoul be provided.\n\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `trimmomatic` and return\nFASTQ file[s] with trimmed adapters, alongside with the uppaired reads FASTQ files (if `lib_type` is set to `PE` and\nsuch files are present after running `trimmomatic`)\nIf input `trigger` is set to `false`, return unchanged `fastq_file_upstream` and `fastq_file_downstream`, previously\nstaged into output directory.\n\nBefore execution `baseCommand`, `fastq_file_upstream` and `fastq_file_downstream` (if provided) are staged into directory\nset as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. They are mount\nto docker container with `ro` mode as part of `--workdir`, because all generated files will have `trimmed` suffix\nin their names, so the staged files will not be overwritten.\n\nTrigger logic is implemented in a bash scripts set by default as `bash_script` input. If the first argument $0 (which is\n`trigger` input) is true, run `trimmomatic` with the rest of the arguments. If $0 is not true, skip `trimmomatic` and\nreturn `fastq_file_upstream` and `fastq_file_downstream` (if provided) staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing in script logic.\n\n`default_output_name` function is used for generating output filename based on `input_file.basename` and provided\nextension.\n","run":"../tools/trimmomatic.cwl","runType":"COMMANDLINETOOL","sources":{"trimmomatic":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/trigger":{"sourceIDs":["fastqc_results_trigger_1"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/lib_type":{"defaultVal":"\\\"PE\\\""},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/adapters_file":{"sourceIDs":["illumina_adapters_file"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/fastq_file_upstream":{"sourceIDs":["sra_to_fastq"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/fastq_file_downstream":{"sourceIDs":["sra_to_fastq"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#trimmomatic/illuminaclip_step_param":{"defaultVal":"\\\"2:30:15\\\""}}},"sra_to_fastq":{"doc":"Tool runs fastq-dump from NCBI SRA toolkit\nSupports only file inputs.\nOutput file names are formed on the base of `sra_file` input basename.\n","run":"../tools/fastq-dump.cwl","runType":"COMMANDLINETOOL","sources":{"sra_to_fastq":{"sourceIDs":["sra_input_file"]},"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl#sra_to_fastq/split_files":{"defaultVal":"true"}}}},"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    \"threads\" [fillcolor=\"#94DDF4\",label=\"threads\"];\n    \"sra_input_file\" [fillcolor=\"#94DDF4\",label=\"sra_input_file\"];\n    \"illumina_adapters_file\" [fillcolor=\"#94DDF4\",label=\"illumina_adapters_file\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"upstream_fastq\" [fillcolor=\"#94DDF4\",label=\"upstream_fastq\"];\n    \"downstream_fastq\" [fillcolor=\"#94DDF4\",label=\"downstream_fastq\"];\n  }\n  \"trimmomatic\" [label=\"trimmomatic\"];\n  \"fastqc_1\" [label=\"fastqc_1\"];\n  \"sra_to_fastq\" [label=\"sra_to_fastq\"];\n  \"fastqc_2\" [label=\"fastqc_2\"];\n  \"threads\" -> \"trimmomatic\" [label=\"threads\"];\n  \"fastqc_results_trigger_2\" -> \"trimmomatic\" [label=\"trigger\"];\n  \"fastqc_results_trigger_1\" -> \"trimmomatic\" [label=\"trigger\"];\n  \"sra_to_fastq\" -> \"trimmomatic\" [label=\"fastq_file_upstream\"];\n  \"sra_to_fastq\" -> \"trimmomatic\" [label=\"fastq_file_downstream\"];\n  \"default1\" -> \"trimmomatic\" [label=\"illuminaclip_step_param\"];\n  \"default1\" [label=\"\\\"2:30:15\\\"\", fillcolor=\"#D5AEFC\"];\n  \"default2\" -> \"trimmomatic\" [label=\"lib_type\"];\n  \"default2\" [label=\"\\\"PE\\\"\", fillcolor=\"#D5AEFC\"];\n  \"illumina_adapters_file\" -> \"trimmomatic\" [label=\"adapters_file\"];\n  \"fastqc_1\" -> \"fastqc_results_trigger_1\" [label=\"summary_file\"];\n  \"sra_to_fastq\" -> \"fastqc_1\" [label=\"fastq_file\"];\n  \"sra_input_file\" -> \"sra_to_fastq\" [label=\"sra_file\"];\n  \"default3\" -> \"sra_to_fastq\" [label=\"split_files\"];\n  \"default3\" [label=\"true\", fillcolor=\"#D5AEFC\"];\n  \"sra_to_fastq\" -> \"fastqc_2\" [label=\"fastq_file\"];\n  \"fastqc_2\" -> \"fastqc_results_trigger_2\" [label=\"summary_file\"];\n  \"trimmomatic\" -> \"upstream_fastq\";\n  \"trimmomatic\" -> \"downstream_fastq\";\n}\n","permalink":"https://w3id.org/cwl/view/git/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/Barski-lab/workflows/blob/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","visualisationPng":"/graph/png/github.com/Barski-lab/workflows/blob/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","visualisationSvg":"/graph/svg/github.com/Barski-lab/workflows/blob/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl","roBundle":"/robundle/github.com/Barski-lab/workflows/blob/744117c1332359de1ed0d2c3c4f314ffcb6797d3/subworkflows/xenbase-sra-to-fastq-pe.cwl"}