From f25566538cb35eef305585763f0fb3c193fd8dc7 Mon Sep 17 00:00:00 2001
From: Vlad Kondratiev <vlad.kondratiev@gmail.com>
Date: Fri, 12 May 2023 09:05:52 +0200
Subject: [PATCH] adjusted cwl workflow to treat
*_ldv_psrfits_requantisation.log files the same way as *rfifind.log files
---
steps/requantize.cwl | 9 ++-------
.../download_and_run_psrfits_requantisation.cwl | 17 -----------------
workflow/psrfits_requantisation.cwl | 4 ----
3 files changed, 2 insertions(+), 28 deletions(-)
diff --git a/steps/requantize.cwl b/steps/requantize.cwl
index e78d79c..a386198 100644
--- a/steps/requantize.cwl
+++ b/steps/requantize.cwl
@@ -39,9 +39,10 @@ outputs:
- '*/*/SAP*/BEAM*/*.png'
- '*/*.png'
- '*.png'
- - rawvoltages/SAP*/BEAM*/*.png
+ - 'rawvoltages/SAP*/BEAM*/*.png'
- '*stokes/SAP*/BEAM*/*.png'
- '*.rfifind.log'
+ - '*stokes/SAP*/BEAM*/*_ldv_psrfits_requantisation.log'
- id: file_content
doc: file_content
type: File
@@ -51,12 +52,6 @@ outputs:
type: File
outputBinding:
glob: '*-ldv-summary.log'
-- id: summary_psrfits_file
- doc: summary_psrfits_file
- type: File?
- outputBinding:
- glob:
- - '*stokes/SAP*/BEAM*/*_ldv_psrfits_requantisation.log'
baseCommand:
- psrfits_requantisation
diff --git a/workflow/download_and_run_psrfits_requantisation.cwl b/workflow/download_and_run_psrfits_requantisation.cwl
index fc4ff99..367a6c2 100644
--- a/workflow/download_and_run_psrfits_requantisation.cwl
+++ b/workflow/download_and_run_psrfits_requantisation.cwl
@@ -22,9 +22,6 @@ outputs:
- id: summary_file
type: File[]
outputSource: requantise/summary_file
-- id: summary_psrfits_file
- type: File[]?
- outputSource: requantise/summary_psrfits_file
- id: ingest
type: Any
outputSource: requantise/ingest
@@ -49,7 +46,6 @@ steps:
run: psrfits_requantisation.cwl
out:
- id: summary_file
- - id: summary_psrfits_file
- id: summary
- id: tar_archive
- id: ingest
@@ -63,21 +59,8 @@ steps:
run: ../steps/join_contents.cwl
out:
- id: summary_file
-- id: join_contents_psrfits
- in:
- - id: summary_files
- source: requantise/summary_psrfits_file
- pickValue: all_non_null
- - id: metadata
- source: requantise/summary
- run: ../steps/join_contents.cwl
- when: $(inputs.summary_files.length > 0)
- out:
- - id: summary_file
- id: format_quality
in:
- - id: summary_psrfits_file
- source: join_contents_psrfits/summary_file
- id: summary_file
source: join_contents/summary_file
- id: plots
diff --git a/workflow/psrfits_requantisation.cwl b/workflow/psrfits_requantisation.cwl
index be17af1..1983ca8 100644
--- a/workflow/psrfits_requantisation.cwl
+++ b/workflow/psrfits_requantisation.cwl
@@ -22,9 +22,6 @@ outputs:
- id: summary_file
type: File
outputSource: requantise/summary_file
-- id: summary_psrfits_file
- type: File?
- outputSource: requantise/summary_psrfits_file
- id: plots
type: File[]
outputSource: requantise/plots
@@ -42,7 +39,6 @@ steps:
- id: file_content
- id: summary
- id: summary_file
- - id: summary_psrfits_file
- id: bf_archive
- id: plots
--
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