diff --git a/workflow/main.nf b/workflow/main.nf
index 068006ee9220087ced6bbc078dd29540e3d2baff..85cce33b1e724886f4bffebab2209d8533e03122 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -92,11 +92,13 @@ process checkDesignFile {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
python $baseDir/scripts/check_design.py -d $designFile -f $readsList
"""
}
@@ -134,11 +136,15 @@ process trimReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load trimgalore/0.4.1
python3 $baseDir/scripts/trim_reads.py -f ${reads[0]} ${reads[1]} -s $sampleId -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load trimgalore/0.4.1
python3 $baseDir/scripts/trim_reads.py -f ${reads[0]} -s $sampleId
"""
}
@@ -148,6 +154,7 @@ process trimReads {
// Align trimmed reads using bwa
process alignReads {
+ queue '128GB,256GB,256GBv1'
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: 'copy'
@@ -166,11 +173,17 @@ process alignReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load bwa/intel/0.7.12
+ module load samtools/1.6
python3 $baseDir/scripts/map_reads.py -f ${reads[0]} ${reads[1]} -r ${index}/genome.fa -s $sampleId -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load bwa/intel/0.7.12
+ module load samtools/1.6
python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa -s $sampleId
"""
}
@@ -180,6 +193,7 @@ process alignReads {
// Dedup reads using sambamba
process filterReads {
+ queue '128GB,256GB,256GBv1'
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: 'copy'
@@ -200,11 +214,19 @@ process filterReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load samtools/1.6
+ module load sambamba/0.6.6
+ module load bedtools/2.26.0
python3 $baseDir/scripts/map_qc.py -b $mapped -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load samtools/1.6
+ module load sambamba/0.6.6
+ module load bedtools/2.26.0
python3 $baseDir/scripts/map_qc.py -b $mapped
"""
}
@@ -221,6 +243,7 @@ dedupReads
// Quality Metrics using deeptools
process experimentQC {
+ queue '128GB,256GB,256GBv1'
publishDir "$outDir/${task.process}", mode: 'copy'
input:
@@ -235,6 +258,8 @@ process experimentQC {
script:
"""
+ module load python/3.6.1-2-anaconda
+ module load deeptools/2.5.0.1
python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign -e $extendReadsLen
"""
@@ -243,6 +268,7 @@ process experimentQC {
// Convert reads to bam
process convertReads {
+ queue '128GB,256GB,256GBv1'
tag "$sampleId-$replicate"
publishDir "$outDir/${task.process}/${sampleId}", mode: 'copy'
@@ -259,11 +285,17 @@ process convertReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load samtools/1.6
+ module load bedtools/2.26.0
python3 $baseDir/scripts/convert_reads.py -b $deduped -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load samtools/1.6
+ module load bedtools/2.26.0
python3 $baseDir/scripts/convert_reads.py -b $deduped
"""
}
@@ -290,6 +322,8 @@ process crossReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load phantompeakqualtools/1.2
python3 $baseDir/scripts/xcor.py -t $seTagAlign -p
"""
}
@@ -323,6 +357,7 @@ process defineExpDesignFiles {
script:
"""
+ module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/experiment_design.py -d $xcorDesign
"""
@@ -348,11 +383,13 @@ process poolAndPsuedoReads {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c $cutoffRatio -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
python3 $baseDir/scripts/pool_and_psuedoreplicate.py -d $experimentObjs -c $cutoffRatio
"""
}
@@ -383,11 +420,21 @@ process callPeaksMACS {
if (pairedEnd) {
"""
+ module load python/3.6.1-2-anaconda
+ module load macs/2.1.0-20151222
+ module load UCSC_userApps/v317
+ module load bedtools/2.26.0
+ module load phantompeakqualtools/1.2
python3 $baseDir/scripts/call_peaks_macs.py -t $tagAlign -x $xcor -c $controlTagAlign -s $sampleId -g $genomeSize -z $chromSizes -p
"""
}
else {
"""
+ module load python/3.6.1-2-anaconda
+ module load macs/2.1.0-20151222
+ module load UCSC_userApps/v317
+ module load bedtools/2.26.0
+ module load phantompeakqualtools/1.2
python3 $baseDir/scripts/call_peaks_macs.py -t $tagAlign -x $xcor -c $controlTagAlign -s $sampleId -g $genomeSize -z $chromSizes
"""
}
@@ -423,6 +470,8 @@ process consensusPeaks {
script:
"""
+ module load python/3.6.1-2-anaconda
+ module load bedtools/2.26.0
python3 $baseDir/scripts/overlap_peaks.py -d $peaksDesign -f $preDiffDesign
"""
@@ -445,6 +494,7 @@ process peakAnnotation {
script:
"""
+ module load R/3.3.2-gccmkl
Rscript $baseDir/scripts/annotate_peaks.R $designAnnotatePeaks $genome
"""
@@ -466,11 +516,13 @@ process motifSearch {
file('version_*.txt') into motifSearchVersions
when:
+
!skipMotif
script:
"""
+ module load R/3.3.2-gccmkl
python3 $baseDir/scripts/motif_search.py -d $designMotifSearch -g $fasta -p $topPeakCount
"""
}
@@ -498,10 +550,15 @@ process diffPeaks {
file('version_*.txt') into diffPeaksVersions
when:
+
noUniqueExperiments > 1 && !skipDiff
script:
+
"""
+ module load python/3.6.1-2-anaconda
+ module load meme/4.11.1-gcc-openmpi
+ module load bedtools/2.26.0
Rscript $baseDir/scripts/diff_peaks.R $designDiffPeaks
"""
}
@@ -536,6 +593,5 @@ 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 -o software_versions
-
"""
}