From 7b47be12cb12950853e251e88c8b2076c5c2ac1a Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 15 Apr 2019 11:52:49 -0500
Subject: [PATCH] Add in software output.
---
workflow/main.nf | 33 ++++++++++++---------------------
1 file changed, 12 insertions(+), 21 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 2526efc..3408dea 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -491,17 +491,17 @@ process softwareReport {
input:
- file 'trimReads_vf/*txt' from trimReadsVersions.first()
- file 'alignReads_vf/*' from alignReadsVersions.first()
- file 'filterReads_vf/*' from filterReadsVersions.first()
- file 'convertReads_vf/*' from convertReadsVersions.first()
- file 'crossReads_vf/*' from crossReadsVersions.first()
- file 'callPeaksMACS_vf/*' from callPeaksMACSVersions.first()
- file 'consensusPeaks_vf/*' from consensusPeaksVersions.first()
- file 'peakAnnotation_vf/*' from peakAnnotationVersions.first()
- file 'motifSearch_vf/*' from motifSearchVersions.first().ifEmpty()
- file 'diffPeaks_vf/*' from diffPeaksVersions.first().ifEmpty()
- file 'experimentQC_vf/*' from experimentQCVersions.first()
+ file trimReads_vf from trimReadsVersions.collect().first()
+ file alignReads_vf from alignReadsVersions.collect().first()
+ file filterReads_vf from filterReadsVersions.collect().first()
+ file convertReads_vf from convertReadsVersions.collect().first()
+ file crossReads_vf from crossReadsVersions.collect().first()
+ file callPeaksMACS_vf from callPeaksMACSVersions.collect().first()
+ file consensusPeaks_vf from consensusPeaksVersions.collect().first()
+ file peakAnnotation_vf from peakAnnotationVersions.collect().first()
+ file motifSearch_vf from motifSearchVersions.collect().first().ifEmpty()
+ file diffPeaks_vf from diffPeaksVersions.collect().first().ifEmpty()
+ file experimentQC_vf from experimentQCVersions.collect().first()
output:
@@ -512,16 +512,7 @@ process softwareReport {
"""
echo $workflow.nextflow.version > version_nextflow.txt
python3 $baseDir/scripts/generate_references.py -r $references -o software_references
- python3 $baseDir/scripts/generate_versions.py -f $trimReads_vf \
- $alignReads_vf \
- $filterReads_vf \
- $convertReads_vf \
- $crossReads_vf \
- $callPeaksMACS_vf \
- $consensusPeaks_vf \
- $motifSearch_vf \
- $diffPeaks_vf \
- $experimentQC_vf \
+ python3 $baseDir/scripts/generate_versions.py -f version*txt \
version_nextflow.txt \
-o software_versions
--
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