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Commit 6a2d842c authored by Venkat Malladi's avatar Venkat Malladi
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Fix syntax and readlines.

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......@@ -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
......
......@@ -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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