cwlVersion: v1.0 label: "gp_makeblastdb" class: Workflow requirements: - class: StepInputExpressionRequirement inputs: asn_cache: Directory[] asnb: File? asnt: File? dbtype: string fasta: File? hardmask: File? softmask: File? title: string ids: File? steps: actual: run: class: CommandLineTool baseCommand: gp_makeblastdb inputs: asn_cache: type: Directory[] inputBinding: prefix: -asn-cache itemSeparator: "," asnb: type: File? inputBinding: prefix: -asnb asnt: type: File? inputBinding: prefix: -asnt dbtype: type: string inputBinding: prefix: -dbtype fasta: type: File? inputBinding: prefix: -fasta found_ids_output_file: # -found-ids-output out/found_ids.txt \ type: string default: found_ids.txt inputBinding: prefix: -found-ids-output found_ids_output_manifest: # -found-ids-output-manifest out/found_ids.mft \ type: string default: found_ids.mft inputBinding: prefix: -found-ids-output-manifest hardmask: # -hardmask-manifest inp/hardmask_data.mft type: File? inputBinding: prefix: -hardmask output_db_file: type: string default: blastdb inputBinding: prefix: -db output_db_manifest: type: string default: blastdb.mft inputBinding: prefix: -output-manifest softmask: # -softmask-manifest inp/softmask_data.mft \ type: File? inputBinding: prefix: -softmask title: # -title 'BLASTdb created by GPipe' type: string inputBinding: prefix: -title ids: type: File? inputBinding: prefix: -ids outputs: dbname: type: string outputBinding: outputEval: $(inputs.output_db_file) found_ids: type: File outputBinding: glob: $(inputs.found_ids_output_file) blastfiles: type: File[] outputBinding: glob: "blastdb.*" # string literal here must match ${output_db_file} in: asn_cache: asn_cache asnb: asnb asnt: asnt dbtype: dbtype fasta: fasta hardmask: hardmask # -hardmask-manifest inp/hardmask_data.mft softmask: softmask # -softmask-manifest inp/softmask_data.mft \ title: title # -title 'BLASTdb created by GPipe' ids: ids out: [blastfiles] mkdir: run: class: CommandLineTool requirements: - class: ShellCommandRequirement arguments: - shellQuote: false valueFrom: >- mkdir $(inputs.blastdir) && cp inputs: blastfiles: type: File[] inputBinding: position: 1 blastdir: type: string inputBinding: position: 2 outputs: blastdb: type: Directory outputBinding: glob: $(inputs.blastdir) in: blastfiles: actual/blastfiles blastdir: default: blastdir out: [blastdb] outputs: blastdb: type: Directory outputSource: mkdir/blastdb