From 6cbc074d20f264c741fd2c83c182f081aaf215ba Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 5 Jan 2019 22:34:24 -0600
Subject: [PATCH] Add option for outdir.
---
workflow/main.nf | 30 ++++++++++++++++--------------
1 file changed, 16 insertions(+), 14 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 4fa5d9f..4b1fa5b 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -13,6 +13,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
params.cutoffRatio = 1.2
+params.outDir= "$outDir"
// Check inputs
if( params.bwaIndex ){
@@ -36,10 +37,11 @@ designFile = params.designFile
genomeSize = params.genomeSize
chromSizes = params.chromSizes
cutoffRatio = params.cutoffRatio
+outDir = params.outDir
process checkDesignFile {
- publishDir "$baseDir/output/design", mode: 'copy'
+ publishDir "$outDir/design", mode: 'copy'
input:
@@ -80,7 +82,7 @@ rawReads = designFilePaths
process trimReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -110,7 +112,7 @@ process trimReads {
process alignReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -141,7 +143,7 @@ process alignReads {
process filterReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -174,13 +176,13 @@ process filterReads {
dedupReads
.map{ sampleId, bam, bai, experimentId, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$bam\t$bai\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
-.collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+.collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
.into { dedupDesign; preDiffDesign }
// Quality Metrics using deeptools
process experimentQC {
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -202,7 +204,7 @@ process experimentQC {
process convertReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -231,7 +233,7 @@ process convertReads {
process crossReads {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -261,12 +263,12 @@ process crossReads {
xcorDesign = xcorReads
.map{ sampleId, seTagAlign, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$seTagAlign\t$tagAlign\t$xcor\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
- .collectFile(name:'design_xcor.tsv', seed:"sample_id\tse_tag_align\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+ .collectFile(name:'design_xcor.tsv', seed:"sample_id\tse_tag_align\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
// Make Experiment design files to be read in for downstream analysis
process defineExpDesignFiles {
- publishDir "$baseDir/output/design", mode: 'copy'
+ publishDir "$outDir/design", mode: 'copy'
input:
@@ -290,7 +292,7 @@ process poolAndPsuedoReads {
tag "${experimentObjs.baseName}"
- publishDir "$baseDir/output/design", mode: 'copy'
+ publishDir "$outDir/design", mode: 'copy'
input:
@@ -324,7 +326,7 @@ experimentRows = experimentPoolObjs
process callPeaksMACS {
tag "$sampleId-$replicate"
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
set sampleId, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId, controlTagAlign from experimentRows
@@ -352,12 +354,12 @@ process callPeaksMACS {
peaksDesign = experimentPeaks
.map{ sampleId, peak, fcSignal, pvalueSignal, experimentId, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$peak\t$fcSignal\t$pvalueSignal\t$experimentId\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
- .collectFile(name:'design_peak.tsv', seed:"sample_id\tpeaks\tfc_signal\tpvalue_signal\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
+ .collectFile(name:'design_peak.tsv', seed:"sample_id\tpeaks\tfc_signal\tpvalue_signal\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$outDir/design")
// Calculate Consensus Peaks
process consensusPeaks {
- publishDir "$baseDir/output/${task.process}", mode: 'copy'
+ publishDir "$outDir/${task.process}", mode: 'copy'
input:
--
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