{"@id":"https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/NAL-i5K/Organism_Onboarding.git","branch":"e332b88ced14c57ec7a0f2edbdcd61afb1228e77","path":"flow_download/workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/NAL-i5K/Organism_Onboarding/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","url":"https://github.com/NAL-i5K/Organism_Onboarding/blob/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl"},"retrievedOn":"2026-10-17T17:35:05.447+00:00","lastCommit":"e332b88ced14c57ec7a0f2edbdcd61afb1228e77","label":"workflow.cwl","inputs":{"url_cds_fasta":{"type":"String[]"},"path_cds_fasta":{"type":"File (Optional)"},"url_genomic_gff":{"type":"String[]"},"path_genomic_gff":{"type":"File (Optional)"},"url_md5checksums":{"type":"String[] (Optional)"},"url_genomic_fasta":{"type":"String[]"},"url_protein_fasta":{"type":"String[]"},"path_genomic_fasta":{"type":"File (Optional)"},"path_protein_fasta":{"type":"File (Optional)"},"url_transcript_fasta":{"type":"String[]"},"path_transcript_fasta":{"type":"File (Optional)"}},"outputs":{"url_string":{"type":"String"},"OUT_cds_fasta":{"type":"File"},"OUT_genomic_gff":{"type":"File"},"OUT_md5checksums":{"type":"File"},"OUT_genomic_fasta":{"type":"File"},"OUT_protein_fasta":{"type":"File"},"OUT_transcript_fasta":{"type":"File"}},"steps":{"wget_cds_fasta":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_cds_fasta":{"sourceIDs":["url_cds_fasta"]}}},"wget_genomic_gff":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_genomic_gff":{"sourceIDs":["url_genomic_gff"]}}},"wget_md5checksums":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_md5checksums":{"sourceIDs":["conditional-wget-md5"]},"https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#wget_md5checksums/in_url":{"sourceIDs":["url_md5checksums"]}}},"wget_genomic_fasta":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_genomic_fasta":{"sourceIDs":["url_genomic_fasta"]}}},"wget_protein_fasta":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_protein_fasta":{"sourceIDs":["url_protein_fasta"]}}},"conditional-wget-md5":{"run":"c2e715b158f4bcb5ebad7a4c891c0d9e","runType":"COMMANDLINETOOL","sources":{"conditional-wget-md5":{"sourceIDs":["url_genomic_gff"]},"https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl#conditional-wget-md5/all_url":{"sourceIDs":["url_cds_fasta"]}}},"wget_transcript_fasta":{"run":"wget_single.cwl","runType":"COMMANDLINETOOL","sources":{"wget_transcript_fasta":{"sourceIDs":["url_transcript_fasta"]}}}},"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    \"url_genomic_gff\" [fillcolor=\"#94DDF4\",label=\"url_genomic_gff\"];\n    \"url_genomic_fasta\" [fillcolor=\"#94DDF4\",label=\"url_genomic_fasta\"];\n    \"url_transcript_fasta\" [fillcolor=\"#94DDF4\",label=\"url_transcript_fasta\"];\n    \"url_protein_fasta\" [fillcolor=\"#94DDF4\",label=\"url_protein_fasta\"];\n    \"path_genomic_gff\" [fillcolor=\"#94DDF4\",label=\"path_genomic_gff\"];\n    \"path_genomic_fasta\" [fillcolor=\"#94DDF4\",label=\"path_genomic_fasta\"];\n    \"path_protein_fasta\" [fillcolor=\"#94DDF4\",label=\"path_protein_fasta\"];\n    \"path_cds_fasta\" [fillcolor=\"#94DDF4\",label=\"path_cds_fasta\"];\n    \"path_transcript_fasta\" [fillcolor=\"#94DDF4\",label=\"path_transcript_fasta\"];\n    \"url_md5checksums\" [fillcolor=\"#94DDF4\",label=\"url_md5checksums\"];\n    \"url_cds_fasta\" [fillcolor=\"#94DDF4\",label=\"url_cds_fasta\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"OUT_genomic_fasta\" [fillcolor=\"#94DDF4\",label=\"OUT_genomic_fasta\"];\n    \"OUT_protein_fasta\" [fillcolor=\"#94DDF4\",label=\"OUT_protein_fasta\"];\n    \"url_string\" [fillcolor=\"#94DDF4\",label=\"url_string\"];\n    \"OUT_genomic_gff\" [fillcolor=\"#94DDF4\",label=\"OUT_genomic_gff\"];\n    \"OUT_cds_fasta\" [fillcolor=\"#94DDF4\",label=\"OUT_cds_fasta\"];\n    \"OUT_md5checksums\" [fillcolor=\"#94DDF4\",label=\"OUT_md5checksums\"];\n    \"OUT_transcript_fasta\" [fillcolor=\"#94DDF4\",label=\"OUT_transcript_fasta\"];\n  }\n  \"conditional-wget-md5\" [label=\"conditional-wget-md5\"];\n  \"wget_cds_fasta\" [label=\"wget_cds_fasta\"];\n  \"wget_md5checksums\" [label=\"wget_md5checksums\"];\n  \"wget_transcript_fasta\" [label=\"wget_transcript_fasta\"];\n  \"wget_genomic_fasta\" [label=\"wget_genomic_fasta\"];\n  \"wget_protein_fasta\" [label=\"wget_protein_fasta\"];\n  \"wget_genomic_gff\" [label=\"wget_genomic_gff\"];\n  \"url_genomic_gff\" -> \"conditional-wget-md5\" [label=\"all_url\"];\n  \"url_genomic_fasta\" -> \"conditional-wget-md5\" [label=\"all_url\"];\n  \"url_transcript_fasta\" -> \"conditional-wget-md5\" [label=\"all_url\"];\n  \"url_protein_fasta\" -> \"conditional-wget-md5\" [label=\"all_url\"];\n  \"url_cds_fasta\" -> \"conditional-wget-md5\" [label=\"all_url\"];\n  \"url_cds_fasta\" -> \"wget_cds_fasta\" [label=\"in_url\"];\n  \"conditional-wget-md5\" -> \"wget_md5checksums\" [label=\"url_string\"];\n  \"url_md5checksums\" -> \"wget_md5checksums\" [label=\"in_url\"];\n  \"url_transcript_fasta\" -> \"wget_transcript_fasta\" [label=\"in_url\"];\n  \"url_genomic_fasta\" -> \"wget_genomic_fasta\" [label=\"in_url\"];\n  \"url_protein_fasta\" -> \"wget_protein_fasta\" [label=\"in_url\"];\n  \"url_genomic_gff\" -> \"wget_genomic_gff\" [label=\"in_url\"];\n  \"wget_genomic_fasta\" -> \"OUT_genomic_fasta\";\n  \"wget_protein_fasta\" -> \"OUT_protein_fasta\";\n  \"conditional-wget-md5\" -> \"url_string\";\n  \"wget_genomic_gff\" -> \"OUT_genomic_gff\";\n  \"wget_cds_fasta\" -> \"OUT_cds_fasta\";\n  \"wget_md5checksums\" -> \"OUT_md5checksums\";\n  \"wget_transcript_fasta\" -> \"OUT_transcript_fasta\";\n}\n","permalink":"https://w3id.org/cwl/view/git/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/NAL-i5K/Organism_Onboarding/blob/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","visualisationPng":"/graph/png/github.com/NAL-i5K/Organism_Onboarding/blob/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","visualisationSvg":"/graph/svg/github.com/NAL-i5K/Organism_Onboarding/blob/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl","roBundle":"/robundle/github.com/NAL-i5K/Organism_Onboarding/blob/e332b88ced14c57ec7a0f2edbdcd61afb1228e77/flow_download/workflow.cwl"}