#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: SubworkflowFeatureRequirement: {} MultipleInputFeatureRequirement: {} InlineJavascriptRequirement: {} StepInputExpressionRequirement: {} ScatterFeatureRequirement: {} inputs: fasta: File IPS_table: File diamond_table: File hmmscan_table: File antismash_geneclusters_txt: File? rna: File cds: File go_config: [string?, File?] eggnog_orthologs: File eggnog_annotations: File output_gff_gz: File output_gff_index: File ko_file: [string, File] diamond_header: string hmmsearch_header: string ips_header: string crisprcas_fasta: File crisprcas_gff: File outputs: functional_annotation_folder: type: Directory outputSource: move_to_functional_annotation_folder/out stats: type: Directory outputSource: post_processing/stats summary_antismash: type: File? outputSource: post_processing/summary_antismash steps: # GO SUMMARY; PFAM; summaries and stats IPS, HMMScan, Pfam; add header; chunking TSV post_processing: run: ../functional-annotation/post-proccessing-go-pfam-stats-subwf.cwl in: fasta: fasta IPS_table: IPS_table go_config: go_config hmmscan_table: hmmscan_table diamond_table: diamond_table antismash_geneclusters_txt: antismash_geneclusters_txt rna: rna cds: cds ko_file: ko_file diamond_header: diamond_header hmmsearch_header: hmmsearch_header ips_header: ips_header out: - stats - summary_antismash - summary_pfam - summary_ko - summary_ips - go_summary - go_summary_slim - chunked_tsvs # << gzip functional annotation files >> compression_func_ann: run: ../../../utils/pigz/gzip.cwl scatter: uncompressed_file in: uncompressed_file: source: - eggnog_annotations - eggnog_orthologs linkMerge: merge_flattened out: [compressed_file] # move FUNCTIONAL-ANNOTATION move_to_functional_annotation_folder: run: ../../../utils/return_directory/return_directory.cwl in: file_list: source: - output_gff_gz - output_gff_index - compression_func_ann/compressed_file - post_processing/summary_ips - post_processing/summary_ko - post_processing/summary_pfam - post_processing/go_summary - post_processing/go_summary_slim - post_processing/chunked_tsvs - crisprcas_fasta - crisprcas_gff linkMerge: merge_flattened dir_name: { default: functional-annotation } out: [ out ] $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: - name: "EMBL - European Bioinformatics Institute" - url: "https://www.ebi.ac.uk/"