{"@id":"https://w3id.org/cwl/view/git/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","retrievedFrom":{"repoUrl":"https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2.git","branch":"2f7764f063e198fd8601229105922f913ea89941","path":"PreProcessing/batch-preprocess-ont.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/fjrmoreews/cwl-workflow-SARS-CoV-2/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","url":"https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl"},"retrievedOn":"2026-10-19T15:54:37.024+00:00","lastCommit":"2f7764f063e198fd8601229105922f913ea89941","label":"batch-preprocess-ont.cwl","inputs":{"ref_human_genome":{"type":"File"},"illumina_accessions":{"type":"String[]"}},"outputs":{"fastqc_zip":{"type":"File[]"},"multiqc_zips":{"type":"File[]"},"multiqc_htmls":{"type":"File[]"},"fastqc_summary":{"type":"File[]"},"original_fastq1":{"type":"File[]"},"processed_fastq":{"type":"File"}},"steps":{"main":{"run":"preprocess-ont.cwl","runType":"WORKFLOW","sources":{"main":{"sourceIDs":["illumina_accessions"]},"https://w3id.org/cwl/view/git/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl#main/ref_human_genome":{"sourceIDs":["ref_human_genome"]}}},"merge_bam":{"doc":"Merge multiple BAM files.\n","run":"../bio-cwl-tools/samtools/samtools_merge.cwl","runType":"COMMANDLINETOOL","sources":{"merge_bam":{"sourceIDs":["main"]}}},"samtools_fastq":{"doc":"Bam to fastq conversion\n","run":"../bio-cwl-tools/samtools/samtools_fastq.cwl","runType":"COMMANDLINETOOL","sources":{"samtools_fastq":{"sourceIDs":["merge_bam"]}}}},"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    \"illumina_accessions\" [fillcolor=\"#94DDF4\",label=\"illumina_accessions\"];\n    \"ref_human_genome\" [fillcolor=\"#94DDF4\",label=\"ref_human_genome\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"fastqc_summary\" [fillcolor=\"#94DDF4\",label=\"fastqc_summary\"];\n    \"fastqc_zip\" [fillcolor=\"#94DDF4\",label=\"fastqc_zip\"];\n    \"multiqc_zips\" [fillcolor=\"#94DDF4\",label=\"multiqc_zips\"];\n    \"processed_fastq\" [fillcolor=\"#94DDF4\",label=\"processed_fastq\"];\n    \"original_fastq1\" [fillcolor=\"#94DDF4\",label=\"original_fastq1\"];\n    \"multiqc_htmls\" [fillcolor=\"#94DDF4\",label=\"multiqc_htmls\"];\n  }\n  \"merge_bam\" [label=\"merge_bam\"];\n  \"samtools_fastq\" [label=\"samtools_fastq\"];\n  \"main\" [label=\"main\", fillcolor=\"#F3CEA1\"];\n  \"main\" -> \"merge_bam\" [label=\"bams\"];\n  \"merge_bam\" -> \"samtools_fastq\" [label=\"bam_sorted\"];\n  \"illumina_accessions\" -> \"main\" [label=\"illumina_accession\"];\n  \"ref_human_genome\" -> \"main\" [label=\"ref_human_genome\"];\n  \"main\" -> \"fastqc_summary\";\n  \"main\" -> \"fastqc_zip\";\n  \"main\" -> \"multiqc_zips\";\n  \"samtools_fastq\" -> \"processed_fastq\";\n  \"main\" -> \"original_fastq1\";\n  \"main\" -> \"multiqc_htmls\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","visualisationPng":"/graph/png/github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","visualisationSvg":"/graph/svg/github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","roBundle":"/robundle/github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/blob/2f7764f063e198fd8601229105922f913ea89941/PreProcessing/batch-preprocess-ont.cwl","licenseName":"MIT License"}