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Commit f09d75cc authored by Timo Millenaar's avatar Timo Millenaar
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Make dppp step optional, depending on whether the data was already compressed

parent bcb8f3d9
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1 merge request!4Make dppp step optional, depending on whether the data was already compressed
...@@ -23,7 +23,7 @@ outputs: ...@@ -23,7 +23,7 @@ outputs:
outputSource: outputSource:
- inspect_step/inspect_file - inspect_step/inspect_file
- id: logfile - id: logfile
type: File[] type: File[]?
outputSource: outputSource:
- dppp/logfile - dppp/logfile
- id: compressed - id: compressed
...@@ -45,6 +45,9 @@ outputs: ...@@ -45,6 +45,9 @@ outputs:
- id: keep_input - id: keep_input
type: boolean type: boolean
outputSource: identify_issues/skip_compress outputSource: identify_issues/skip_compress
- id: input_storage_manager
type: string
outputSource: identify_issues/input_storage_manager
steps: steps:
- id: identify_issues - id: identify_issues
...@@ -60,6 +63,7 @@ steps: ...@@ -60,6 +63,7 @@ steps:
- unfixable_issues - unfixable_issues
- msout - msout
- skip_compress - skip_compress
- input_storage_manager
- id: fix_ai_2013 - id: fix_ai_2013
in: in:
- id: msin - id: msin
...@@ -106,7 +110,10 @@ steps: ...@@ -106,7 +110,10 @@ steps:
- id: extract_sip_meta - id: extract_sip_meta
in: in:
- id: msin - id: msin
source: dppp/msout source:
- dppp/msout
- msin
pickValue: first_non_null
- id: compressed_file - id: compressed_file
source: compress/compressed source: compress/compressed
- id: skip - id: skip
...@@ -131,6 +138,9 @@ steps: ...@@ -131,6 +138,9 @@ steps:
default: Dysco default: Dysco
- id: databitrate - id: databitrate
default: 10 default: 10
- id: input_storage_manager
source: identify_issues/input_storage_manager
when: $(inputs.input_storage_manager != "DyscoStorageManager")
run: steps/DPPP.cwl run: steps/DPPP.cwl
out: out:
- id: msout - id: msout
...@@ -164,7 +174,10 @@ steps: ...@@ -164,7 +174,10 @@ steps:
label: compress label: compress
in: in:
- id: directory - id: directory
source: dppp/msout source:
- dppp/msout
- msin
pickValue: first_non_null
- id: skip - id: skip
source: identify_issues/skip_compress source: identify_issues/skip_compress
when: $(inputs.skip == false) when: $(inputs.skip == false)
...@@ -174,9 +187,15 @@ steps: ...@@ -174,9 +187,15 @@ steps:
- id: inspect_step - id: inspect_step
in: in:
- id: msin - id: msin
source: dppp/msout source:
- dppp/msout
- msin
pickValue: first_non_null
- id: inspect_file_name - id: inspect_file_name
source: dppp/msout source:
- dppp/msout
- msin
pickValue: first_non_null
valueFrom: $(self.basename + "_inspect.h5") valueFrom: $(self.basename + "_inspect.h5")
run: steps/create_inspect_dataset.cwl run: steps/create_inspect_dataset.cwl
out: out:
......
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