Reslove merge conflicts.

workflow/main.nf

@@ -14,18 +14,10 @@ params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
 params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
 params.cutoffRatio = 1.2
+params.outDir= "$baseDir/output"
+params.extendReadsLen = 100
 params.topPeakCount = 600
 
-// Define regular variables
-pairedEnd = params.pairedEnd
-designFile = params.designFile
-genomeSize = params.genomeSize
-genome = params.genome
-chromSizes = params.chromSizes
-fasta = params.fasta
-cutoffRatio = params.cutoffRatio
-topPeakCount = params.topPeakCount
-
 // Check inputs
 if( params.bwaIndex ){
   bwaIndex = Channel
@@ -42,11 +34,21 @@ readsList = Channel
   .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t")}
   .collectFile( name: 'fileList.tsv', newLine: true )
 
+// Define regular variables
+pairedEnd = params.pairedEnd
+designFile = params.designFile
+genomeSize = params.genomeSize
+chromSizes = params.chromSizes
+fasta = params.fasta
+cutoffRatio = params.cutoffRatio
+outDir = params.outDir
+extendReadsLen = params.extendReadsLen
+topPeakCount = params.topPeakCount
 
 // Check design file for errors
 process checkDesignFile {
 
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy'
 
   input:
 
@@ -87,7 +89,7 @@ rawReads = designFilePaths
 process trimReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -117,7 +119,7 @@ process trimReads {
 process alignReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -148,7 +150,7 @@ process alignReads {
 process filterReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -181,13 +183,13 @@ 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:
 
@@ -200,7 +202,7 @@ process experimentQC {
   script:
 
   """
-  python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign
+  python3 $baseDir/scripts/experiment_qc.py -d $dedupDesign -e $extendReadsLen
   """
 
 }
@@ -209,7 +211,7 @@ process experimentQC {
 process convertReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -238,7 +240,7 @@ process convertReads {
 process crossReads {
 
   tag "$sampleId-$replicate"
-  publishDir "$baseDir/output/${task.process}", mode: 'copy'
+  publishDir "$outDir/${task.process}", mode: 'copy'
 
   input:
 
@@ -268,12 +270,12 @@ 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:
 
@@ -297,7 +299,7 @@ process poolAndPsuedoReads {
 
 
   tag "${experimentObjs.baseName}"
-  publishDir "$baseDir/output/design", mode: 'copy'
+  publishDir "$outDir/design", mode: 'copy'
 
   input:
 
@@ -331,7 +333,7 @@ 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
@@ -359,12 +361,12 @@ 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:
 

workflow/scripts/experiment_qc.py

@@ -34,6 +34,11 @@ def get_args():
                         help="The design file to run QC (tsv format).",
                         required=True)
 
+    parser.add_argument('-e', '--extension',
+                        help="Number of base pairs to extend the reads",
+                        type=int,
+                        required=True)
+
     args = parser.parse_args()
     return args
 
@@ -51,7 +56,7 @@ def check_tools():
         raise Exception('Missing deeptools')
 
 
-def generate_read_summary(design):
+def generate_read_summary(design, extension):
     '''Generate summary of data based on read counts.'''
 
     bam_files = ' '.join(design['bam_reads'])
@@ -59,8 +64,8 @@ def generate_read_summary(design):
     mbs_filename = 'sample_mbs.npz'
 
     mbs_command = (
-        "multiBamSummary bins -p %d --bamfiles %s --labels %s -out %s"
-        % (cpu_count(), bam_files, labels, mbs_filename)
+        "multiBamSummary bins -p %d --bamfiles %s --extendReads %d --labels %s -out %s"
+        % (cpu_count(), bam_files, extension, labels, mbs_filename)
         )
 
     logger.info("Running deeptools with %s", mbs_command)
@@ -90,7 +95,7 @@ def check_correlation(mbs):
     out, err = spearman_correlation.communicate()
 
 
-def check_coverage(design):
+def check_coverage(design, extension):
     '''Asses the sequencing depth of samples.'''
 
     bam_files = ' '.join(design['bam_reads'])
@@ -100,8 +105,8 @@ def check_coverage(design):
                     " --ignoreDuplicates --minMappingQuality 10"
 
     coverage_command = (
-        "plotCoverage -b %s --labels %s %s --plotFile %s"
-        % (bam_files, labels, coverage_params, coverage_filename)
+        "plotCoverage -b %s --extendReads %d --labels %s %s --plotFile %s"
+        % (bam_files, extension, labels, coverage_params, coverage_filename)
         )
 
     logger.info("Running deeptools with %s", coverage_command)
@@ -128,14 +133,14 @@ def update_controls(design):
     return design
 
 
-def check_enrichment(sample_id, control_id, sample_reads, control_reads):
+def check_enrichment(sample_id, control_id, sample_reads, control_reads, extension):
     '''Asses the enrichment per sample.'''
 
     fingerprint_filename = sample_id + '_fingerprint.png'
 
     fingerprint_command = (
-        "plotFingerprint -b %s %s --labels %s %s --plotFile %s"
-        % (sample_reads, control_reads, sample_id, control_id, fingerprint_filename)
+        "plotFingerprint -b %s %s --extendReads %d --labels %s %s --plotFile %s"
+        % (sample_reads, control_reads, extension, sample_id, control_id, fingerprint_filename)
         )
 
     logger.info("Running deeptools with %s", fingerprint_command)
@@ -147,6 +152,7 @@ def check_enrichment(sample_id, control_id, sample_reads, control_reads):
 def main():
     args = get_args()
     design = args.design
+    extension = args.extension
 
     # Create a file handler
     handler = logging.FileHandler('experiment_qc.log')
@@ -159,11 +165,11 @@ def main():
     design_df = pd.read_csv(design, sep='\t')
 
     # Run correlation
-    mbs_filename = generate_read_summary(design_df)
+    mbs_filename = generate_read_summary(design_df, extension)
     check_correlation(mbs_filename)
 
     # Run coverage
-    check_coverage(design_df)
+    check_coverage(design_df, extension)
 
     # Run enrichment
     new_design_df = update_controls(design_df)
@@ -172,7 +178,8 @@ def main():
                             row['sample_id'],
                             row['control_id'],
                             row['bam_reads'],
-                            row['control_reads'])
+                            row['control_reads'],
+                            extension)
 
 
 if __name__ == '__main__':