From 020970293890e23b02ec9e24dcdee4fea36acb20 Mon Sep 17 00:00:00 2001
From: Timo Millenaar <tmillenaar@gmail.com>
Date: Thu, 20 Jun 2024 16:35:12 +0200
Subject: [PATCH] Make dppp step optional, depending on whether the data was
already compressed
---
compress_pipeline.cwl | 29 ++++++++++++++++++++++++-----
1 file changed, 24 insertions(+), 5 deletions(-)
diff --git a/compress_pipeline.cwl b/compress_pipeline.cwl
index 3c0385f..41634ee 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:
--
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