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drpatelhdrpatelh
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Add missing header comments to all modules/subworkflows
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‎workflows/chipseq.nf‎

Lines changed: 69 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -182,7 +182,7 @@ workflow CHIPSEQ {
182182
}
183183

184184
//
185-
// SUBWORKFLOW: Alignment with BOWTIE2 & BAM QC
185+
// SUBWORKFLOW: Alignment with Bowtie2 & BAM QC
186186
//
187187
if (params.aligner == 'bowtie2') {
188188
ALIGN_BOWTIE2 (
@@ -199,7 +199,7 @@ workflow CHIPSEQ {
199199
}
200200

201201
//
202-
// SUBWORKFLOW: Alignment with CHROMAP & BAM QC
202+
// SUBWORKFLOW: Alignment with Chromap & BAM QC
203203
//
204204
if (params.aligner == 'chromap') {
205205
ALIGN_CHROMAP (
@@ -210,7 +210,7 @@ workflow CHIPSEQ {
210210

211211
// Filter out paired-end reads until the issue below is fixed
212212
// https://github.com/nf-core/chipseq/issues/291
213-
// ch_genome_bam = ALIGN_CHROMAP.out.bam
213+
// ch_genome_bam = ALIGN_CHROMAP.out.bam
214214
ALIGN_CHROMAP
215215
.out
216216
.bam
@@ -220,9 +220,11 @@ workflow CHIPSEQ {
220220
return [ meta, bam ]
221221
paired_end: !meta.single_end
222222
return [ meta, bam ]
223-
}.set { ch_genome_bam_chromap }
223+
}
224+
.set { ch_genome_bam_chromap }
224225

225-
ch_genome_bam_chromap.paired_end
226+
ch_genome_bam_chromap
227+
.paired_end
226228
.collect()
227229
.map {
228230
it ->
@@ -264,7 +266,7 @@ workflow CHIPSEQ {
264266
}
265267

266268
//
267-
// SUBWORKFLOW: Merge resequenced BAM files
269+
// MODULE: Merge resequenced BAM files
268270
//
269271
ch_genome_bam
270272
.map {
@@ -306,7 +308,7 @@ workflow CHIPSEQ {
306308
ch_versions = ch_versions.mix(FILTER_BAM_BAMTOOLS.out.versions.first().ifEmpty(null))
307309

308310
//
309-
// MODULE: Library coverage
311+
// MODULE: Preseq coverage analysis
310312
//
311313
ch_preseq_multiqc = Channel.empty()
312314
if (!params.skip_preseq) {
@@ -318,7 +320,7 @@ workflow CHIPSEQ {
318320
}
319321

320322
//
321-
// MODULE: Post alignment QC
323+
// MODULE: Picard post alignment QC
322324
//
323325
ch_picardcollectmultiplemetrics_multiqc = Channel.empty()
324326
if (!params.skip_picard_metrics) {
@@ -332,13 +334,16 @@ workflow CHIPSEQ {
332334
}
333335

334336
//
335-
// MODULE: Strand cross-correlation
337+
// MODULE: Phantompeaktools strand cross-correlation and QC metrics
336338
//
337339
PHANTOMPEAKQUALTOOLS (
338340
FILTER_BAM_BAMTOOLS.out.bam
339341
)
340342
ch_versions = ch_versions.mix(PHANTOMPEAKQUALTOOLS.out.versions.first())
341343

344+
//
345+
// MODULE: MultiQC custom content for Phantompeaktools
346+
//
342347
MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS (
343348
PHANTOMPEAKQUALTOOLS.out.spp.join(PHANTOMPEAKQUALTOOLS.out.rdata, by: [0]),
344349
ch_spp_nsc_header,
@@ -347,47 +352,53 @@ workflow CHIPSEQ {
347352
)
348353

349354
//
350-
// MODULE: Coverage tracks
355+
// MODULE: BedGraph coverage tracks
351356
//
352357
BEDTOOLS_GENOMECOV (
353358
FILTER_BAM_BAMTOOLS.out.bam.join(FILTER_BAM_BAMTOOLS.out.flagstat, by: [0])
354359
)
355360
ch_versions = ch_versions.mix(BEDTOOLS_GENOMECOV.out.versions.first())
356361

357362
//
358-
// MODULE: Coverage tracks
363+
// MODULE: BigWig coverage tracks
359364
//
360365
UCSC_BEDGRAPHTOBIGWIG (
361366
BEDTOOLS_GENOMECOV.out.bedgraph,
362367
PREPARE_GENOME.out.chrom_sizes
363368
)
364369
ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first())
365370

366-
//
367-
// MODULE: Coverage plots
368-
//
369371
ch_deeptoolsplotprofile_multiqc = Channel.empty()
370372
if (!params.skip_plot_profile) {
373+
//
374+
// MODULE: deepTools matrix generation for plotting
375+
//
371376
DEEPTOOLS_COMPUTEMATRIX (
372377
UCSC_BEDGRAPHTOBIGWIG.out.bigwig,
373378
PREPARE_GENOME.out.gene_bed
374379
)
375380
ch_versions = ch_versions.mix(DEEPTOOLS_COMPUTEMATRIX.out.versions.first())
376381

382+
//
383+
// MODULE: deepTools profile plots
384+
//
377385
DEEPTOOLS_PLOTPROFILE (
378386
DEEPTOOLS_COMPUTEMATRIX.out.matrix
379387
)
380388
ch_deeptoolsplotprofile_multiqc = DEEPTOOLS_PLOTPROFILE.out.table
381389
ch_versions = ch_versions.mix(DEEPTOOLS_PLOTPROFILE.out.versions.first())
382390

391+
//
392+
// MODULE: deepTools heatmaps
393+
//
383394
DEEPTOOLS_PLOTHEATMAP (
384395
DEEPTOOLS_COMPUTEMATRIX.out.matrix
385396
)
386397
ch_versions = ch_versions.mix(DEEPTOOLS_PLOTHEATMAP.out.versions.first())
387398
}
388399

389400
//
390-
// Refactor channels: [ meta, [ ip_bam, control_bam ] [ ip_bai, control_bai ] ]
401+
// Create channels: [ meta, [ ip_bam, control_bam ] [ ip_bai, control_bai ] ]
391402
//
392403
FILTER_BAM_BAMTOOLS
393404
.out
@@ -404,7 +415,7 @@ workflow CHIPSEQ {
404415
.set { ch_ip_control_bam_bai }
405416

406417
//
407-
// plotFingerprint for IP and control together
418+
// MODULE: deepTools plotFingerprint joint QC for IP and control
408419
//
409420
ch_deeptoolsplotfingerprint_multiqc = Channel.empty()
410421
if (!params.skip_plot_fingerprint) {
@@ -416,7 +427,7 @@ workflow CHIPSEQ {
416427
}
417428

418429
//
419-
// Call peaks
430+
// MODULE: Calculute genome size with khmer
420431
//
421432
ch_macs_gsize = Channel.empty()
422433
ch_custompeaks_frip_multiqc = Channel.empty()
@@ -432,30 +443,33 @@ workflow CHIPSEQ {
432443
ch_macs_gsize = KHMER_UNIQUEKMERS.out.kmers.map { it.text.trim() }
433444
}
434445

435-
// Create channel: [ meta, ip_bam, control_bam ]
446+
// Create channels: [ meta, ip_bam, control_bam ]
436447
ch_ip_control_bam_bai
437448
.map {
438449
meta, bams, bais ->
439450
[ meta , bams[0], bams[1] ]
440451
}
441452
.set { ch_ip_control_bam }
442453

454+
//
455+
// MODULE: Call peaks with MACS2
456+
//
443457
MACS2_CALLPEAK (
444458
ch_ip_control_bam,
445459
ch_macs_gsize
446460
)
447461
ch_versions = ch_versions.mix(MACS2_CALLPEAK.out.versions.first())
448462

449463
//
450-
// Filter for MACS2 files without peaks
464+
// Filter out samples with 0 MACS2 peaks called
451465
//
452466
MACS2_CALLPEAK
453467
.out
454468
.peak
455469
.filter { meta, peaks -> peaks.size() > 0 }
456470
.set { ch_macs2_peaks }
457471

458-
// Create channel: [ meta, ip_bam, peaks ]
472+
// Create channels: [ meta, ip_bam, peaks ]
459473
ch_ip_control_bam
460474
.join(ch_macs2_peaks, by: [0])
461475
.map {
@@ -464,12 +478,15 @@ workflow CHIPSEQ {
464478
}
465479
.set { ch_ip_bam_peaks }
466480

481+
//
482+
// MODULE: Calculate FRiP score
483+
//
467484
FRIP_SCORE (
468485
ch_ip_bam_peaks
469486
)
470487
ch_versions = ch_versions.mix(FRIP_SCORE.out.versions.first())
471488

472-
// Create channel: [ meta, peaks, frip ]
489+
// Create channels: [ meta, peaks, frip ]
473490
ch_ip_bam_peaks
474491
.join(FRIP_SCORE.out.txt, by: [0])
475492
.map {
@@ -478,6 +495,9 @@ workflow CHIPSEQ {
478495
}
479496
.set { ch_ip_peaks_frip }
480497

498+
//
499+
// MODULE: FRiP score custom content for MultiQC
500+
//
481501
MULTIQC_CUSTOM_PEAKS (
482502
ch_ip_peaks_frip,
483503
ch_peak_count_header,
@@ -487,6 +507,9 @@ workflow CHIPSEQ {
487507
ch_custompeaks_count_multiqc = MULTIQC_CUSTOM_PEAKS.out.count
488508

489509
if (!params.skip_peak_annotation) {
510+
| //
511+
// MODULE: Annotate peaks with MACS2
512+
//
490513
HOMER_ANNOTATEPEAKS_MACS2 (
491514
ch_macs2_peaks,
492515
PREPARE_GENOME.out.fasta,
@@ -495,11 +518,17 @@ workflow CHIPSEQ {
495518
ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS_MACS2.out.versions.first())
496519

497520
if (!params.skip_peak_qc) {
521+
//
522+
// MODULE: MACS2 QC plots with R
523+
//
498524
PLOT_MACS2_QC (
499525
ch_macs2_peaks.collect{it[1]}
500526
)
501527
ch_versions = ch_versions.mix(PLOT_MACS2_QC.out.versions)
502528

529+
//
530+
// MODULE: Peak annotation QC plots with R
531+
//
503532
PLOT_HOMER_ANNOTATEPEAKS (
504533
HOMER_ANNOTATEPEAKS_MACS2.out.txt.collect{it[1]},
505534
ch_peak_annotation_header,
@@ -517,7 +546,7 @@ workflow CHIPSEQ {
517546
ch_deseq2_pca_multiqc = Channel.empty()
518547
ch_deseq2_clustering_multiqc = Channel.empty()
519548
if (!params.skip_consensus_peaks) {
520-
// Create channel: [ meta , [ peaks ] ]
549+
// Create channels: [ meta , [ peaks ] ]
521550
// Where meta = [ id:antibody, multiple_groups:true/false, replicates_exist:true/false ]
522551
ch_macs2_peaks
523552
.map {
@@ -543,27 +572,36 @@ workflow CHIPSEQ {
543572
}
544573
.set { ch_antibody_peaks }
545574

575+
//
576+
// MODULE: Generate consensus peaks across samples
577+
//
546578
MACS2_CONSENSUS (
547579
ch_antibody_peaks
548580
)
549581
ch_macs2_consensus_bed_lib = MACS2_CONSENSUS.out.bed
550582
ch_versions = ch_versions.mix(MACS2_CONSENSUS.out.versions)
551583

552584
if (!params.skip_peak_annotation) {
585+
//
586+
// MODULE: Annotate consensus peaks
587+
//
553588
HOMER_ANNOTATEPEAKS_CONSENSUS (
554589
MACS2_CONSENSUS.out.bed,
555590
PREPARE_GENOME.out.fasta,
556591
PREPARE_GENOME.out.gtf
557592
)
558593
ch_versions = ch_versions.mix(HOMER_ANNOTATEPEAKS_CONSENSUS.out.versions)
559594

595+
//
596+
// MODULE: Add boolean fields to annotated consensus peaks to aid filtering
597+
//
560598
ANNOTATE_BOOLEAN_PEAKS (
561599
MACS2_CONSENSUS.out.boolean_txt.join(HOMER_ANNOTATEPEAKS_CONSENSUS.out.txt, by: [0]),
562600
)
563601
ch_versions = ch_versions.mix(ANNOTATE_BOOLEAN_PEAKS.out.versions)
564602
}
565603

566-
// Create channel: [ antibody, [ ip_bams ] ]
604+
// Create channels: [ antibody, [ ip_bams ] ]
567605
ch_ip_control_bam
568606
.map {
569607
meta, ip_bam, control_bam ->
@@ -572,7 +610,7 @@ workflow CHIPSEQ {
572610
.groupTuple()
573611
.set { ch_antibody_bams }
574612

575-
// Create channel: [ meta, [ ip_bams ], saf ]
613+
// Create channels: [ meta, [ ip_bams ], saf ]
576614
MACS2_CONSENSUS
577615
.out
578616
.saf
@@ -587,13 +625,19 @@ workflow CHIPSEQ {
587625
}
588626
.set { ch_saf_bams }
589627

628+
//
629+
// MODULE: Quantify peaks across samples with featureCounts
630+
//
590631
SUBREAD_FEATURECOUNTS (
591632
ch_saf_bams
592633
)
593634
ch_subreadfeaturecounts_multiqc = SUBREAD_FEATURECOUNTS.out.summary
594635
ch_versions = ch_versions.mix(SUBREAD_FEATURECOUNTS.out.versions.first())
595636

596637
if (!params.skip_deseq2_qc) {
638+
//
639+
// MODULE: Generate QC plots with DESeq2
640+
//
597641
DESEQ2_QC (
598642
SUBREAD_FEATURECOUNTS.out.counts,
599643
ch_deseq2_pca_header,
@@ -605,7 +649,7 @@ workflow CHIPSEQ {
605649
}
606650

607651
//
608-
// Create IGV session
652+
// MODULE: Create IGV session
609653
//
610654
if (!params.skip_igv) {
611655
IGV (

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