From bc6e7472ba6054b13422fd0d93f848e0fb8f42c7 Mon Sep 17 00:00:00 2001
From: Matthijs van der Wild <matthijs.van-der-wild@durham.ac.uk>
Date: Fri, 21 Jun 2024 19:56:22 +0000
Subject: [PATCH] Write results to cwl.output.json to bypass size restrictions
---
steps/filter_ms_group.cwl | 26 +++++++++-----------------
1 file changed, 9 insertions(+), 17 deletions(-)
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
index 73ae7909..83c41c61 100644
--- a/steps/filter_ms_group.cwl
+++ b/steps/filter_ms_group.cwl
@@ -21,19 +21,16 @@ outputs:
- id: output
type: Directory[]
outputBinding:
- loadContents: true
- glob: 'selected_ms.json'
- outputEval: '$(JSON.parse(self[0].contents))'
+ glob: $(runtime.outdir)/cwl.output.json
+ outputEval: $(self.output)
- id: selected_ms
type: string[]
outputBinding:
- loadContents: true
- glob: 'out.json'
- outputEval: $(JSON.parse(self[0].contents).selected_ms)
+ glob: $(runtime.outdir)/cwl.output.json
+ outputEval: $(self.selected_ms)
label: filter_ms_group
requirements:
- - class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: filter_ms_group.py
@@ -50,23 +47,18 @@ requirements:
ms_by_name = { ms.split(os.path.sep)[-1]:
{'class':'Directory', 'path': ms} for ms in ms_list}
- output_file = 'selected_ms.json'
-
with open(json_file, 'r') as f_stream:
selected_ms = json.load(f_stream)[group_id]
selected_ms = [os.path.basename(ms_name) for ms_name in selected_ms]
- cwl_output = {'selected_ms': selected_ms}
+ selected_ms_names = [ms_by_name[ms_name] for ms_name in selected_ms
+ if ms_name != 'dummy.ms']
+ cwl_output = {'selected_ms': selected_ms,
+ 'output': selected_ms_names}
- with open('./out.json', 'w') as fp:
+ with open('./cwl.output.json', 'w') as fp:
json.dump(cwl_output, fp)
- selected_ms = [ms_by_name[ms_name] for ms_name in selected_ms if ms_name != 'dummy.ms']
-
-
- with open(output_file, 'w') as f_stream:
- json.dump(selected_ms, f_stream)
-
hints:
- class: InitialWorkDirRequirement
listing:
--
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