cwlVersion: v1.0 class: Workflow label: functional analysis prediction with InterProScan requirements: - class: SubworkflowFeatureRequirement - class: SchemaDefRequirement types: - $import: ../tools/esl-reformat-replace.yaml - $import: ../tools/InterProScan-apps.yaml - $import: ../tools/InterProScan-protein_formats.yaml inputs: go_summary_config: File predicted_CDS: File outputs: functional_annotations: type: File outputSource: functional_analysis/i5Annotations go_summary: type: File outputSource: summarize_with_GO/go_summary steps: remove_asterisks_and_reformat: run: ../tools/esl-reformat.cwl in: sequences: predicted_CDS replace: { default: { find: '*', replace: X } } out: [ reformatted_sequences ] functional_analysis: doc: | Matches are generated against predicted CDS, using a sub set of databases (Pfam, TIGRFAM, PRINTS, PROSITE patterns, Gene3d) from InterPro. run: ../tools/InterProScan5.21-60.cwl in: proteinFile: remove_asterisks_and_reformat/reformatted_sequences applications: default: - Pfam - TIGRFAM - PRINTS - ProSitePatterns - Gene3D out: [i5Annotations] summarize_with_GO: doc: | A summary of Gene Ontology (GO) terms derived from InterPro matches to the sample. It is generated using a reduced list of GO terms called GO slim (http://www.geneontology.org/ontology/subsets/goslim_metagenomics.obo) run: ../tools/go_summary.cwl in: InterProScan_results: functional_analysis/i5Annotations config: go_summary_config out: [ go_summary ] $namespaces: edam: http://edamontology.org/ s: http://schema.org/ $schemas: - http://edamontology.org/EDAM_1.16.owl - https://schema.org/docs/schema_org_rdfa.html s:license: "https://www.apache.org/licenses/LICENSE-2.0" s:copyrightHolder: "EMBL - European Bioinformatics Institute"