#!/usr/bin/env cwl-runner # Copyright (C) 2018 EMBL - European Bioinformatics Institute # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # http://www.apache.org/licenses/LICENSE-2.0 # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. cwlVersion: v1.0 class: Workflow inputs: email: string sequence: File database: string method: string outformat: string db: string program: string type: string multifasta: string useSeqId: string outf: string outputs: workflow_output: type: type: array items: File outputSource: ncbiblast_step/blast_array_accs steps: phmmer_step: run: 'hmmer3_phmmer.cwl' in: sequence: sequence email: email database: database out: [phmmer_ids] dbfetch_step: run: 'dbfetch-file.cwl' in: accessions: phmmer_step/phmmer_ids method: method outformat: outformat database: db out: [sequences] ncbiblast_step: run: 'ncbiblast.cwl' in: sequence_file: dbfetch_step/sequences email: email database: db program: program type: type multifasta: multifasta useSeqId: useSeqId outformat: outf out: [blast_array_accs]