diff --git a/compress_pipeline.cwl b/compress_pipeline.cwl index 3c0385fc9572e656abd37c114733e3ec504173e7..41634ee811e8e1d650677dfa474a7e086110e00a 100644 --- a/compress_pipeline.cwl +++ b/compress_pipeline.cwl @@ -23,7 +23,7 @@ outputs: outputSource: - inspect_step/inspect_file - id: logfile - type: File[] + type: File[]? outputSource: - dppp/logfile - id: compressed @@ -45,6 +45,9 @@ outputs: - id: keep_input type: boolean outputSource: identify_issues/skip_compress +- id: input_storage_manager + type: string + outputSource: identify_issues/input_storage_manager steps: - id: identify_issues @@ -60,6 +63,7 @@ steps: - unfixable_issues - msout - skip_compress + - input_storage_manager - id: fix_ai_2013 in: - id: msin @@ -106,7 +110,10 @@ steps: - id: extract_sip_meta in: - id: msin - source: dppp/msout + source: + - dppp/msout + - msin + pickValue: first_non_null - id: compressed_file source: compress/compressed - id: skip @@ -131,6 +138,9 @@ steps: default: Dysco - id: databitrate default: 10 + - id: input_storage_manager + source: identify_issues/input_storage_manager + when: $(inputs.input_storage_manager != "DyscoStorageManager") run: steps/DPPP.cwl out: - id: msout @@ -164,7 +174,10 @@ steps: label: compress in: - id: directory - source: dppp/msout + source: + - dppp/msout + - msin + pickValue: first_non_null - id: skip source: identify_issues/skip_compress when: $(inputs.skip == false) @@ -174,9 +187,15 @@ steps: - id: inspect_step in: - id: msin - source: dppp/msout + source: + - dppp/msout + - msin + pickValue: first_non_null - id: inspect_file_name - source: dppp/msout + source: + - dppp/msout + - msin + pickValue: first_non_null valueFrom: $(self.basename + "_inspect.h5") run: steps/create_inspect_dataset.cwl out: