Move modules to main for astrocyte.

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
-
   """
 }