#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: SubworkflowFeatureRequirement: {} MultipleInputFeatureRequirement: {} InlineJavascriptRequirement: {} StepInputExpressionRequirement: {} ScatterFeatureRequirement: {} ResourceRequirement: ramMin: 5000 ramMax: 10000 coresMin: 4 inputs: interproscan_annotation: File hmmscan_annotation: File pfam_annotation: File antismash_gene_clusters: File? rna: File cds: File ko_file: string outputs: stats: outputSource: functional_stats/stats type: Directory summary_ips: outputSource: write_summaries/summary_ips type: File summary_ko: outputSource: write_summaries/summary_ko type: File summary_pfam: outputSource: write_summaries/summary_pfam type: File summary_antismash: outputSource: write_summaries/summary_antismash type: File? steps: functional_stats: run: ../../tools/summaries/functional_stats.cwl in: interproscan: interproscan_annotation hmmscan: hmmscan_annotation pfam: pfam_annotation cmsearch_file: rna cds_file: cds antismash_file: antismash_gene_clusters ko_file: ko_file out: [stats, ips_yaml, ko_yaml, pfam_yaml, antismash_yaml] write_summaries: run: ../../tools/summaries/write_summaries.cwl in: ips_entry_maps: functional_stats/ips_yaml ips_outname: source: cds valueFrom: $(self.nameroot.split('_CDS')[0]).summary.ips ko_entry_maps: functional_stats/ko_yaml ko_outname: source: cds valueFrom: $(self.nameroot.split('_CDS')[0]).summary.ko pfam_entry_maps: functional_stats/pfam_yaml pfam_outname: source: cds valueFrom: $(self.nameroot.split('_CDS')[0]).summary.pfam antismash_entry_maps: functional_stats/antismash_yaml antismash_outname: source: cds valueFrom: $(self.nameroot.split('_CDS')[0]).summary.antismash out: [summary_ips, summary_ko, summary_pfam, summary_antismash] $namespaces: edam: http://edamontology.org/ s: http://schema.org/ $schemas: - http://edamontology.org/EDAM_1.16.owl - https://schema.org/version/latest/schemaorg-current-http.rdf s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"