{"@id":"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","retrievedFrom":{"repoUrl":"https://github.com/MG-RAST/pipeline.git","branch":"f5839797da8209a9d3e441023f88130219751020","path":"CWL/Workflows/qc-basic.workflow.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/MG-RAST/pipeline/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","url":"https://github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl"},"retrievedOn":"2023-04-02T02:33:03.113+00:00","lastCommit":"f5839797da8209a9d3e441023f88130219751020","label":"qc-basic.workflow.cwl","inputs":{"jobid":{"type":"String"},"sequences":{"type":"File"},"kmerLength":{"type":"Integer[] (Optional)"}},"outputs":{"qcStatFile":{"type":"File"},"seqBinFile":{"type":"File"},"seqStatFile":{"type":"File"},"qcSummaryFile":{"type":"File"}},"steps":{"kmer":{"label":"calcualate kmer bins","doc":"Script to use jellyfish to get kmer information\nInput:\\ fasta/fastq file\nOutput:\\ kmer information, one of:\\\n    1. hash:\\ binary hash of counts\n    2. stats:\\ summary stats\n    3. dump:\\ profile (kmer seq - count)\n    4. histo:\\ histogram (count - abundance)\n    5. histo ranked:\\ count, abundance, count*abundance, reverse-sum(abundance), reverse-sum(count*abundance), ratio-to-largest\n","run":"../Tools/kmer-tool.tool.cwl","runType":"COMMANDLINETOOL","sources":{"kmer":{"sourceIDs":["sequences"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#kmer/length":{"sourceIDs":["kmerLength"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#kmer/prefix":{"sourceIDs":["jobid"]}}},"drisee":{"run":"../Tools/drisee.tool.cwl","runType":"COMMANDLINETOOL","sources":{"drisee":{"sourceIDs":["sequences"]}}},"consensus":{"run":"../Tools/consensus.tool.cwl","runType":"COMMANDLINETOOL","sources":{"consensus":{"sourceIDs":["sequenceStats"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#consensus/output":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#consensus/sequences":{"sourceIDs":["sequences"]}}},"formatQcStats":{"run":"../Tools/format_qc_stats.tool.cwl","runType":"COMMANDLINETOOL","sources":{"formatQcStats":{"sourceIDs":["kmer"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatQcStats/consensus":{"sourceIDs":["consensus"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatQcStats/outPrefix":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatQcStats/driseeInfo":{"sourceIDs":["drisee"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatQcStats/driseeStat":{"sourceIDs":["drisee"]}}},"sequenceStats":{"label":"sequence statistics","doc":"Calculate statistics for fasta files.\nOutput fields:\\\n  bp_count\n  sequence_count\n  average_length\n  standard_deviation_length\n  length_min\n  length_max\n  average_gc_content\n  standard_deviation_gc_content\n  average_gc_ratio\n  standard_deviation_gc_ratio\n  ambig_char_count\n  ambig_sequence_count\n  average_ambig_chars\n  sequence_type\n","run":"../Tools/seq_length_stats.tool.cwl","runType":"COMMANDLINETOOL","sources":{"sequenceStats":{"sourceIDs":["sequences"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#sequenceStats/gcBin":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#sequenceStats/lenBin":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#sequenceStats/outName":{"sourceIDs":["jobid"]}}},"formatSequenceStats":{"run":"../Tools/format_seq_stats.tool.cwl","runType":"COMMANDLINETOOL","sources":{"formatSequenceStats":{"sourceIDs":["sequenceStats"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatSequenceStats/sequence_gc":{"sourceIDs":["sequenceStats"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatSequenceStats/output_prefix":{"sourceIDs":["jobid"]},"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl#formatSequenceStats/sequence_stats":{"sourceIDs":["sequenceStats"]}}}},"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    \"sequences\" [fillcolor=\"#94DDF4\",label=\"sequences\"];\n    \"kmerLength\" [fillcolor=\"#94DDF4\",label=\"kmerLength\"];\n    \"jobid\" [fillcolor=\"#94DDF4\",label=\"jobid\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"seqStatFile\" [fillcolor=\"#94DDF4\",label=\"seqStatFile\"];\n    \"seqBinFile\" [fillcolor=\"#94DDF4\",label=\"seqBinFile\"];\n    \"qcSummaryFile\" [fillcolor=\"#94DDF4\",label=\"qcSummaryFile\"];\n    \"qcStatFile\" [fillcolor=\"#94DDF4\",label=\"qcStatFile\"];\n  }\n  \"sequenceStats\" [label=\"sequence statistics\"];\n  \"consensus\" [label=\"consensus\"];\n  \"drisee\" [label=\"drisee\"];\n  \"formatSequenceStats\" [label=\"formatSequenceStats\"];\n  \"kmer\" [label=\"calcualate kmer bins\"];\n  \"formatQcStats\" [label=\"formatQcStats\"];\n  \"sequences\" -> \"sequenceStats\" [label=\"sequences\"];\n  \"jobid\" -> \"sequenceStats\" [label=\"outName\"];\n  \"jobid\" -> \"sequenceStats\" [label=\"lenBin\"];\n  \"jobid\" -> \"sequenceStats\" [label=\"gcBin\"];\n  \"sequenceStats\" -> \"consensus\" [label=\"stats\"];\n  \"sequences\" -> \"consensus\" [label=\"sequences\"];\n  \"jobid\" -> \"consensus\" [label=\"output\"];\n  \"sequences\" -> \"drisee\" [label=\"sequences\"];\n  \"sequenceStats\" -> \"formatSequenceStats\" [label=\"sequence_lengths\"];\n  \"sequenceStats\" -> \"formatSequenceStats\" [label=\"sequence_stats\"];\n  \"sequenceStats\" -> \"formatSequenceStats\" [label=\"sequence_gc\"];\n  \"jobid\" -> \"formatSequenceStats\" [label=\"output_prefix\"];\n  \"sequences\" -> \"kmer\" [label=\"sequences\"];\n  \"kmerLength\" -> \"kmer\" [label=\"length\"];\n  \"jobid\" -> \"kmer\" [label=\"prefix\"];\n  \"kmer\" -> \"formatQcStats\" [label=\"kmer\"];\n  \"consensus\" -> \"formatQcStats\" [label=\"consensus\"];\n  \"drisee\" -> \"formatQcStats\" [label=\"driseeInfo\"];\n  \"drisee\" -> \"formatQcStats\" [label=\"driseeStat\"];\n  \"jobid\" -> \"formatQcStats\" [label=\"outPrefix\"];\n  \"formatSequenceStats\" -> \"seqStatFile\";\n  \"formatSequenceStats\" -> \"seqBinFile\";\n  \"formatQcStats\" -> \"qcSummaryFile\";\n  \"formatQcStats\" -> \"qcStatFile\";\n}\n","licenseLink":"https://spdx.org/licenses/BSD-2-Clause","packed":false,"permalink":"https://w3id.org/cwl/view/git/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","visualisationXdot":"/graph/xdot/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","roBundle":"/robundle/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","licenseName":"BSD 2-clause \"Simplified\" License","visualisationPng":"/graph/png/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl","visualisationSvg":"/graph/svg/github.com/MG-RAST/pipeline/blob/f5839797da8209a9d3e441023f88130219751020/CWL/Workflows/qc-basic.workflow.cwl"}