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Resolve "Pool and Pseudoreplication"

Merged Resolve "Pool and Pseudoreplication"
13-poolandpseudo into master
Merged Venkat Malladi requested to merge 13-poolandpseudo into master
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workflow/main.nf
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@@ -65,11 +65,11 @@ process checkDesignFile {
if (pairedEnd) {
rawReads = designFilePaths
.splitCsv(sep: '\t', header: true)
.map { row -> [ row.sample_id, [row.fastq_read1, row.fastq_read2], row.biosample, row.factor, row.treatment, row.replicate, row.control_id ] }
.map { row -> [ row.sample_id, [row.fastq_read1, row.fastq_read2], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate, row.control_id ] }
} else {
rawReads = designFilePaths
.splitCsv(sep: '\t', header: true)
.map { row -> [ row.sample_id, [row.fastq_read1], row.biosample, row.factor, row.treatment, row.replicate, row.control_id ] }
.map { row -> [ row.sample_id, [row.fastq_read1], row.experiment_id, row.biosample, row.factor, row.treatment, row.replicate, row.control_id ] }
}
// Trim raw reads using trimgalore
@@ -80,11 +80,11 @@ process trimReads {
input:
set sampleId, reads, biosample, factor, treatment, replicate, controlId from rawReads
set sampleId, reads, experimentId biosample, factor, treatment, replicate, controlId from rawReads
output:
set sampleId, file('*.fq.gz'), biosample, factor, treatment, replicate, controlId into trimmedReads
set sampleId, file('*.fq.gz'), experimentId, biosample, factor, treatment, replicate, controlId into trimmedReads
file('*trimming_report.txt') into trimgalore_results
script:
@@ -110,12 +110,12 @@ process alignReads {
input:
set sampleId, reads, biosample, factor, treatment, replicate, controlId from trimmedReads
set sampleId, reads, experimentId, biosample, factor, treatment, replicate, controlId from trimmedReads
file index from bwaIndex.first()
output:
set sampleId, file('*.bam'), biosample, factor, treatment, replicate, controlId into mappedReads
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into mappedReads
file '*.srt.bam.flagstat.qc' into mappedReadsStats
script:
@@ -141,12 +141,12 @@ process filterReads {
input:
set sampleId, mapped, biosample, factor, treatment, replicate, controlId from mappedReads
set sampleId, mapped, experimentId, biosample, factor, treatment, replicate, controlId from mappedReads
output:
set sampleId, file('*.bam'), file('*.bai'), biosample, factor, treatment, replicate, controlId into dedupReads
set sampleId, file('*.bam'), biosample, factor, treatment, replicate, controlId into convertReads
set sampleId, file('*.bam'), file('*.bai'), experimentId, biosample, factor, treatment, replicate, controlId into dedupReads
set sampleId, file('*.bam'), experimentId, biosample, factor, treatment, replicate, controlId into convertReads
file '*flagstat.qc' into dedupReadsStats
file '*pbc.qc' into dedupReadsComplexity
file '*dup.qc' into dupReads
@@ -168,9 +168,9 @@ process filterReads {
// Define channel collecting dedup reads intp new design file
dedupDesign = dedupReads
.map{ sampleId, bam, bai, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$bam\t$bai\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
.collectFile(name:'design_dedup.tsv', seed:"sample_id\tbam_reads\tbam_index\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
.map{ sampleId, bam, bai, experimentId, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$bam\t$bai\texperimentId\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")
// Quality Metrics using deeptools
process experimentQC {
@@ -201,11 +201,11 @@ process convertReads {
input:
set sampleId, deduped, biosample, factor, treatment, replicate, controlId from convertReads
set sampleId, deduped, experimentId, biosample, factor, treatment, replicate, controlId from convertReads
output:
set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), biosample, factor, treatment, replicate, controlId into tagReads
set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), experimentId, biosample, factor, treatment, replicate, controlId into tagReads
script:
@@ -230,11 +230,11 @@ process crossReads {
input:
set sampleId, seTagAlign, tagAlign, biosample, factor, treatment, replicate, controlId from tagReads
set sampleId, seTagAlign, tagAlign, experimentId, biosample, factor, treatment, replicate, controlId from tagReads
output:
set sampleId, tagAlign, file('*.cc.qc'), biosample, factor, treatment, replicate, controlId into xcorReads
set sampleId, tagAlign, file('*.cc.qc'), experimentId, biosample, factor, treatment, replicate, controlId into xcorReads
set file('*.cc.qc'), file('*.cc.plot.pdf') into xcorReadsStats
script:
@@ -254,9 +254,9 @@ process crossReads {
// Define channel collecting tagAlign and xcor into design file
xcorDesign = xcorReads
.map{ sampleId, tagAlign, xcor, biosample, factor, treatment, replicate, controlId ->
"$sampleId\t$tagAlign\t$xcor\t$biosample\t$factor\t$treatment\t$replicate\t$controlId\n"}
.collectFile(name:'design_xcor.tsv', seed:"sample_id\ttag_align\txcor\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
.map{ sampleId, tagAlign, xcor, experimentId, biosample, factor, treatment, replicate, controlId ->
"$sampleId\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\ttag_align\txcor\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\n", storeDir:"$baseDir/output/design")
// Make Experiment design files to be read in for downstream analysis
process defineExpDesignFiles {