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Make dppp step optional, depending on whether the data was already compressed

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+ 24
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@@ -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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