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Commit 1dbc04a

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JoseEspinosaJoseEspinosa
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Merge remote-tracking branch 'upstream/dev' into fixes
2 parents dde0ce7 + d8b98cd commit 1dbc04a

2 files changed

Lines changed: 22 additions & 58 deletions

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‎conf/modules.config‎

Lines changed: 0 additions & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -108,7 +108,6 @@ process {
108108
// Read QC and trimming options
109109
//
110110

111-
if (!(params.skip_fastqc || params.skip_qc)) {
112111
process {
113112
withName: 'FASTQC' {
114113
ext.args = '--quiet'
@@ -126,9 +125,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
126125
]
127126
}
128127
}
129-
}
130128

131-
if (!params.skip_trimming) {
132129
process {
133130
withName: 'TRIMGALORE' {
134131
ext.args = {
@@ -166,7 +163,6 @@ if (!params.skip_trimming) {
166163
]
167164
}
168165
}
169-
}
170166

171167
process {
172168
withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
@@ -199,7 +195,6 @@ process {
199195
}
200196
}
201197

202-
if (params.aligner == 'bwa') {
203198
process {
204199
withName: 'BWA_MEM' {
205200
ext.args = {
@@ -219,9 +214,7 @@ if (params.aligner == 'bwa') {
219214
]
220215
}
221216
}
222-
}
223217

224-
if (params.aligner == 'bowtie2') {
225218
process {
226219
withName: 'BOWTIE2_ALIGN' {
227220
ext.args = {
@@ -247,9 +240,7 @@ if (params.aligner == 'bowtie2') {
247240
]
248241
}
249242
}
250-
}
251243

252-
if (params.aligner == 'chromap') {
253244
process {
254245
withName: 'CHROMAP_INDEX' {
255246
publishDir = [
@@ -271,9 +262,7 @@ if (params.aligner == 'chromap') {
271262
]
272263
}
273264
}
274-
}
275265

276-
if (params.aligner == 'star') {
277266
process {
278267
withName: '.*:ALIGN_STAR:STAR_ALIGN' {
279268
ext.args = [
@@ -307,7 +296,6 @@ if (params.aligner == 'star') {
307296
]
308297
}
309298
}
310-
}
311299

312300
process {
313301
withName: 'PICARD_MERGESAMFILES' {
@@ -487,7 +475,6 @@ process {
487475
}
488476
}
489477

490-
if (!params.skip_picard_metrics) {
491478
process {
492479
withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
493480
ext.args = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
@@ -506,9 +493,7 @@ if (!params.skip_picard_metrics) {
506493
]
507494
}
508495
}
509-
}
510496

511-
if (!params.skip_preseq) {
512497
process {
513498
withName: 'PRESEQ_LCEXTRAP' {
514499
ext.args = '-verbose -bam -seed 1'
@@ -520,9 +505,7 @@ if (!params.skip_preseq) {
520505
]
521506
}
522507
}
523-
}
524508

525-
if (!params.skip_plot_profile) {
526509
process {
527510
withName: 'DEEPTOOLS_COMPUTEMATRIX' {
528511
ext.args = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
@@ -552,9 +535,7 @@ if (!params.skip_plot_profile) {
552535
]
553536
}
554537
}
555-
}
556538

557-
if (!params.skip_plot_fingerprint) {
558539
process {
559540
withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
560541
ext.args = { [
@@ -570,7 +551,6 @@ if (!params.skip_plot_fingerprint) {
570551
]
571552
}
572553
}
573-
}
574554

575555
process {
576556
withName: 'MACS3_CALLPEAK' {
@@ -606,7 +586,6 @@ process {
606586
}
607587
}
608588

609-
if (!params.skip_peak_annotation) {
610589
process {
611590
withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER:HOMER_ANNOTATEPEAKS' {
612591
ext.args = '-gid'
@@ -619,7 +598,6 @@ if (!params.skip_peak_annotation) {
619598
}
620599
}
621600

622-
if (!params.skip_peak_qc) {
623601
process {
624602
withName: 'PLOT_MACS3_QC' {
625603
ext.args = '-o ./ -p macs3_peak'
@@ -640,10 +618,7 @@ if (!params.skip_peak_annotation) {
640618
]
641619
}
642620
}
643-
}
644-
}
645621

646-
if (!params.skip_consensus_peaks) {
647622
process {
648623
withName: 'MACS3_CONSENSUS' {
649624
ext.when = { meta.multiple_groups || meta.replicates_exist }
@@ -666,7 +641,6 @@ if (!params.skip_consensus_peaks) {
666641
}
667642
}
668643

669-
if (!params.skip_peak_annotation) {
670644
process {
671645
withName: '.*:BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2:HOMER_ANNOTATEPEAKS' {
672646
ext.args = '-gid'
@@ -687,9 +661,7 @@ if (!params.skip_consensus_peaks) {
687661
]
688662
}
689663
}
690-
}
691664

692-
if (!params.skip_deseq2_qc) {
693665
process {
694666
withName: 'DESEQ2_QC' {
695667
ext.when = { meta.multiple_groups && meta.replicates_exist }
@@ -707,10 +679,7 @@ if (!params.skip_consensus_peaks) {
707679
]
708680
}
709681
}
710-
}
711-
}
712682

713-
if (!params.skip_igv) {
714683
process {
715684
withName: 'IGV' {
716685
publishDir = [
@@ -727,9 +696,7 @@ if (!params.skip_igv) {
727696
]
728697
}
729698
}
730-
}
731699

732-
if (!params.skip_multiqc) {
733700
process {
734701
withName: 'MULTIQC' {
735702
ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
@@ -740,4 +707,3 @@ if (!params.skip_multiqc) {
740707
]
741708
}
742709
}
743-
}

‎workflows/chipseq.nf‎

Lines changed: 22 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -61,30 +61,6 @@ include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_m
6161
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6262
*/
6363

64-
// JSON files required by BAMTools for alignment filtering
65-
ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
66-
ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
67-
68-
// Header files for MultiQC
69-
ch_spp_nsc_header = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
70-
ch_spp_rsc_header = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
71-
ch_spp_correlation_header = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
72-
ch_peak_count_header = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
73-
ch_frip_score_header = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
74-
ch_peak_annotation_header = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
75-
ch_deseq2_pca_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
76-
ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))
77-
78-
// Save AWS IGenomes file containing annotation version
79-
def anno_readme = params.genomes[ params.genome ]?.readme
80-
if (anno_readme && file(anno_readme).exists()) {
81-
file("${params.outdir}/genome/").mkdirs()
82-
file(anno_readme).copyTo("${params.outdir}/genome/")
83-
}
84-
85-
86-
// // Info required for completion email and summary
87-
// def multiqc_report = []
8864

8965
workflow CHIPSEQ {
9066

@@ -103,6 +79,28 @@ workflow CHIPSEQ {
10379
ch_star_index // channel: path(star/index/)
10480

10581
main:
82+
83+
// JSON files required by BAMTools for alignment filtering
84+
ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
85+
ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
86+
87+
// Header files for MultiQC
88+
ch_spp_nsc_header = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
89+
ch_spp_rsc_header = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
90+
ch_spp_correlation_header = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
91+
ch_peak_count_header = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
92+
ch_frip_score_header = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
93+
ch_peak_annotation_header = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
94+
ch_deseq2_pca_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
95+
ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))
96+
97+
// Save AWS IGenomes file containing annotation version
98+
def anno_readme = params.genomes[ params.genome ]?.readme
99+
if (anno_readme && file(anno_readme).exists()) {
100+
file("${params.outdir}/genome/").mkdirs()
101+
file(anno_readme).copyTo("${params.outdir}/genome/")
102+
}
103+
106104
ch_multiqc_files = channel.empty()
107105

108106
//

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