#!/usr/bin/env cwl-runner class: Workflow cwlVersion: v1.2 doc: | Assemble a set of reads using SKESA requirements: - class: MultipleInputFeatureRequirement inputs: reads: File? srr: string? report_usage: boolean no_internet: type: boolean? make_uuid: type: boolean? default: true uuid_in: type: File? output_name: type: string? default: contigs.out outputs: contigs: type: File outputSource: skesa_assemble/contigs_out uuid_out: type: File outputSource: ping_start/uuid_out steps: ping_start: run: progs/pinger.cwl in: report_usage: report_usage make_uuid: make_uuid uuid_in: uuid_in state: default: "start" workflow: default: "skesa" instring: output_name out: [stdout, outstring, uuid_out] skesa_assemble: run: progs/skesa.cwl in: reads: reads sra_run: srr contigs_out_name: ping_start/outstring out: [contigs_out] ping_stop: run: progs/pinger.cwl in: report_usage: report_usage uuid_in: ping_start/uuid_out state: default: "stop" workflow: default: "skesa" # Note: the input on the following line should be the same as all of the outputs # for this workflow, so we ensure this is the final step. infile: - ping_start/stdout - skesa_assemble/contigs_out out: [stdout]