diff --git a/steps/bulk_rename.cwl b/steps/bulk_rename.cwl index eaae4ab154eeeb3c379080c4a37f79793d9ccb5f..9102a16c2b80e11c577082a1b0f2498319eb2779 100644 --- a/steps/bulk_rename.cwl +++ b/steps/bulk_rename.cwl @@ -15,12 +15,11 @@ inputs: type: string - id: file_suffix type: string? - default: log outputs: - id: output - type: File + type: 'File[]' outputBinding: - glob: "$(inputs.file_prefix).$(inputs.file_suffix)" + glob: "tmp/$(inputs.file_prefix)*" label: bulk_rename requirements: - class: InitialWorkDirRequirement @@ -32,6 +31,9 @@ requirements: FILE_LIST=("\${@}") FILE_PREFIX=$(inputs.file_prefix) FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix) - cat "\${FILE_LIST[@]}" > "\$FILE_PREFIX.\$FILE_SUFFIX" + mkdir tmp + for i in "\${!FILE_LIST[@]}"; do + cp "\${FILE_LIST[\$i]}" "tmp/\${FILE_PREFIX}_\${i}\${FILE_SUFFIX}" + done writable: false - - class: InlineJavascriptRequirement + - class: InlineJavascriptRequirement \ No newline at end of file diff --git a/steps/concatenate_files.cwl b/steps/concatenate_files.cwl new file mode 100644 index 0000000000000000000000000000000000000000..eaae4ab154eeeb3c379080c4a37f79793d9ccb5f --- /dev/null +++ b/steps/concatenate_files.cwl @@ -0,0 +1,37 @@ +class: CommandLineTool +cwlVersion: v1.0 +$namespaces: + sbg: 'https://www.sevenbridges.com/' +id: bulk_rename +baseCommand: + - bash + - bulk_rename.sh +inputs: + - id: file_list + type: 'File[]' + inputBinding: + position: 0 + - id: file_prefix + type: string + - id: file_suffix + type: string? + default: log +outputs: + - id: output + type: File + outputBinding: + glob: "$(inputs.file_prefix).$(inputs.file_suffix)" +label: bulk_rename +requirements: + - class: InitialWorkDirRequirement + listing: + - entryname: bulk_rename.sh + entry: | + #!/bin/bash + set -e + FILE_LIST=("\${@}") + FILE_PREFIX=$(inputs.file_prefix) + FILE_SUFFIX=$(inputs.file_suffix === null ? '' : inputs.file_suffix) + cat "\${FILE_LIST[@]}" > "\$FILE_PREFIX.\$FILE_SUFFIX" + writable: false + - class: InlineJavascriptRequirement diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl index 14b4f250c49d401aa44f9581215b63ba194718cf..d5d273ad0afb7fac99cfb9d1e77a5fb6bbf8bb80 100644 --- a/workflows/HBA_calibrator.cwl +++ b/workflows/HBA_calibrator.cwl @@ -1,6 +1,6 @@ class: Workflow cwlVersion: v1.0 -id: _h_b_a_calibrator +id: HBA_calibrator label: HBA_calibrator $namespaces: sbg: 'https://www.sevenbridges.com/' @@ -73,7 +73,7 @@ inputs: 'sbg:y': -500 - id: maxStddev type: float? - default: -1 + default: -1.0 'sbg:x': -1000 'sbg:y': -400 - id: solutions2transfer @@ -160,7 +160,7 @@ inputs: 'sbg:y': 1200 - id: max_separation_arcmin type: float? - default: 1 + default: 1.0 'sbg:x': -1000 'sbg:y': 1300 - id: calibrator_path_skymodel @@ -319,7 +319,7 @@ steps: default: dppp_prep_cal out: - id: output - run: ./../steps/bulk_rename.cwl + run: ./../steps/concatenate_files.cwl label: concat_logfiles 'sbg:x': 500 'sbg:y': 1000