{"@id":"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","retrievedFrom":{"repoUrl":"https://github.com/Barski-lab/workflows.git","branch":"f371e588940e65889febaea9c35bc96c9e1558c3","path":"tools/genome-kallisto-index.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/Barski-lab/workflows/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","url":"https://github.com/Barski-lab/workflows/blob/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl"},"retrievedOn":"2026-09-28T10:13:46.592+00:00","lastCommit":"f371e588940e65889febaea9c35bc96c9e1558c3","label":"genome-kallisto-index.cwl","doc":"Generates a FASTA file with the DNA sequences for all transcripts in a GFF file and builds kallisto index\n","inputs":{"kmer_size":{"doc":"k-mer (odd) length (default: 31, max value: 31)\n","type":"Integer (Optional)"},"make_unique":{"doc":"Replace repeated target names with unique names\n","type":"Boolean (Optional)"},"genome_fasta_file":{"doc":"Genome file in FASTA format, uncompressed\n","type":"File"},"annotation_gtf_file":{"doc":"GTF annotation file\n","type":"File"},"index_output_filename":{"doc":"Filename for the kallisto index to be constructed\n","type":"String (Optional)"}},"outputs":{"kallisto_index":{"type":"File"},"kallisto_stderr_log":{"type":"File"},"kallisto_stdout_log":{"type":"File"},"transcriptome_fasta_file":{"type":"File"}},"steps":{"generate_transcriptome":{"doc":"Generates a FASTA file with the DNA sequences for all transcripts in a GFF file\n","run":"gffread.cwl","runType":"COMMANDLINETOOL","sources":{"generate_transcriptome":{"sourceIDs":["annotation_gtf_file"]},"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl#generate_transcriptome/genome_fasta_file":{"sourceIDs":["genome_fasta_file"]}}},"generate_kallisto_index":{"doc":"kallisto index builds an index from a FASTA formatted file of target sequences\n","run":"kallisto-index.cwl","runType":"COMMANDLINETOOL","sources":{"generate_kallisto_index":{"sourceIDs":["kmer_size"]},"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl#generate_kallisto_index/make_unique":{"sourceIDs":["make_unique"]},"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl#generate_kallisto_index/output_filename":{"sourceIDs":["index_output_filename"]},"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl#generate_kallisto_index/transcriptome_fasta_file":{"sourceIDs":["generate_transcriptome"]}}}},"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    \"index_output_filename\" [fillcolor=\"#94DDF4\",label=\"index_output_filename\"];\n    \"make_unique\" [fillcolor=\"#94DDF4\",label=\"make_unique\"];\n    \"annotation_gtf_file\" [fillcolor=\"#94DDF4\",label=\"annotation_gtf_file\"];\n    \"genome_fasta_file\" [fillcolor=\"#94DDF4\",label=\"genome_fasta_file\"];\n    \"kmer_size\" [fillcolor=\"#94DDF4\",label=\"kmer_size\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"kallisto_stdout_log\" [fillcolor=\"#94DDF4\",label=\"kallisto_stdout_log\"];\n    \"kallisto_index\" [fillcolor=\"#94DDF4\",label=\"kallisto_index\"];\n    \"kallisto_stderr_log\" [fillcolor=\"#94DDF4\",label=\"kallisto_stderr_log\"];\n    \"transcriptome_fasta_file\" [fillcolor=\"#94DDF4\",label=\"transcriptome_fasta_file\"];\n  }\n  \"generate_transcriptome\" [label=\"generate_transcriptome\"];\n  \"generate_kallisto_index\" [label=\"generate_kallisto_index\"];\n  \"annotation_gtf_file\" -> \"generate_transcriptome\" [label=\"annotation_gtf_file\"];\n  \"genome_fasta_file\" -> \"generate_transcriptome\" [label=\"genome_fasta_file\"];\n  \"kmer_size\" -> \"generate_kallisto_index\" [label=\"kmer_size\"];\n  \"generate_transcriptome\" -> \"generate_kallisto_index\" [label=\"transcriptome_fasta_file\"];\n  \"make_unique\" -> \"generate_kallisto_index\" [label=\"make_unique\"];\n  \"index_output_filename\" -> \"generate_kallisto_index\" [label=\"output_filename\"];\n  \"generate_kallisto_index\" -> \"kallisto_stdout_log\";\n  \"generate_kallisto_index\" -> \"kallisto_index\";\n  \"generate_kallisto_index\" -> \"kallisto_stderr_log\";\n  \"generate_transcriptome\" -> \"transcriptome_fasta_file\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/Barski-lab/workflows/blob/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","visualisationPng":"/graph/png/github.com/Barski-lab/workflows/blob/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","visualisationSvg":"/graph/svg/github.com/Barski-lab/workflows/blob/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","roBundle":"/robundle/github.com/Barski-lab/workflows/blob/f371e588940e65889febaea9c35bc96c9e1558c3/tools/genome-kallisto-index.cwl","licenseName":"Apache License 2.0"}