From 92096435391380a2ebfe2d877816a501eedfc221 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 5 Jan 2019 07:35:53 -0600
Subject: [PATCH] Change order of process. Made diffPeaks a when opperative.
---
workflow/main.nf | 53 ++++++++++++++++++++----------------------------
1 file changed, 22 insertions(+), 31 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 7e421c7..4d32304 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -387,9 +387,6 @@ process consensusPeaks {
}
-// Define channel to find number of unique experiments
-noUniqueExperiments = uniqueExperiments.splitCsv(sep: '\t', header: true).toList()
-
// Annotate Peaks
process peakAnnotation {
@@ -411,57 +408,51 @@ process peakAnnotation {
}
-
-// Calculate Differential Binding Activity
-process diffPeaks {
+// Motif Search Peaks
+process motifSearch {
publishDir "$baseDir/output/${task.process}", mode: 'copy'
input:
- file designDiffPeaks
+ file designMotifSearch
output:
- file '*_diffbind.bed' into diffPeaks
- file '*_diffbind.csv' into diffPeaksCounts
- file '*.pdf' into diffPeaksStats
- file 'normcount_peaksets.txt' into normCountPeaks
+ file "*memechip" into motifSearch
script:
- if (noUniqueExperiments.size() == 1) {
- """
- touch no_diffbind.bed
- touch no_diffbind.csv
- touch no_heatmap.pdf
- touch no_pca.pdf
- touch normcount_peaksets.txt
- """
- }
- else {
- """
- Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
- """
- }
+ """
+ python3 $baseDir/scripts/motif_search.py -d $designMotifSearch -g $fasta -p $topPeakCount
+ """
}
-// Motif Search Peaks
-process motifSearch {
+// Define channel to find number of unique experiments
+noUniqueExperiments = uniqueExperiments.splitCsv(sep: '\t', header: true).toList()
+
+// Calculate Differential Binding Activity
+process diffPeaks {
publishDir "$baseDir/output/${task.process}", mode: 'copy'
input:
- file designMotifSearch
+ file designDiffPeaks
output:
- file "*memechip" into motifSearch
+ file '*_diffbind.bed' into diffPeaks
+ file '*_diffbind.csv' into diffPeaksCounts
+ file '*.pdf' into diffPeaksStats
+ file 'normcount_peaksets.txt' into normCountPeaks
+
+ when:
+ noUniqueExperiments.size() > 1
- script:
+ script:
"""
- python3 $baseDir/scripts/motif_search.py -d $designMotifSearch -g $fasta -p $topPeakCount
+ Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
"""
}
--
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