From 6a2d842c248c20b18f2b132b2504972a3cfe081b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 14 Aug 2018 13:21:10 -0500
Subject: [PATCH] Fix syntax and readlines.
---
workflow/main.nf | 17 +++++++----------
workflow/scripts/overlap_peaks.py | 2 +-
2 files changed, 8 insertions(+), 11 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index db15eb3..75a25de 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -371,10 +371,9 @@ process consensusPeaks {
file '*.replicated.*' into consensusPeaks
file '*.rejected.*' into rejectedPeaks
- file("design_diffPeaks.csv") into designDiffPeaks
- file("design_annotatePeaks.tsv") into designAnnotatePeaks
- file("design_annotatePeaks.tsv") into designMotifSearch
- file("unqiue_experiments.csv") into uniqueExperiments
+ file 'design_diffPeaks.csv' into designDiffPeaks
+ file 'design_annotatePeaks.tsv' into designAnnotatePeaks, designMotifSearch
+ file 'unique_experiments.csv' into uniqueExperiments
script:
@@ -386,8 +385,7 @@ process consensusPeaks {
// Define channel to find number of unique experiments
noUniqueExperiments = Channel
- .from(uniqueExperiments)
- .readLines()
+ .from(uniqueExperiments.readLines())
.size()
// Annotate Peaks
@@ -423,10 +421,9 @@ process diffPeaks {
output:
- file "design_diffpeak_annotatePeaks.tsv" into diffPeaksDesignAnnotatePeaks
- file "design_diffpeak_annotatePeaks.tsv" into diffPeaksDesignMeme
- file "*_diffbind.bed" into diffPeaks
- file "*_diffbind.csv" into diffPeaksCounts
+ file 'design_diffpeak_annotatePeaks.tsv' into diffPeaksDesignAnnotatePeaks, diffPeaksDesignMeme
+ file '*_diffbind.bed' into diffPeaks
+ file '*_diffbind.csv' into diffPeaksCounts
file '*.pdf' into diffPeaksStats
file 'normcount_peaksets.txt' into normCountPeaks
diff --git a/workflow/scripts/overlap_peaks.py b/workflow/scripts/overlap_peaks.py
index bb7b53d..ad0d57e 100644
--- a/workflow/scripts/overlap_peaks.py
+++ b/workflow/scripts/overlap_peaks.py
@@ -213,7 +213,7 @@ def main():
# Write the unique conditions
unique_experiments = pd.Series(design_diff['Condition'].unique)
- unique_experiments.to_csv('unqiue_experiments.csv')
+ unique_experiments.to_csv('unique_experiments.csv')
if __name__ == '__main__':
--
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