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JoseEspinosaJoseEspinosa
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Merge pull request nf-core#491 from nf-core/fix-strict-syntax
Fix strict syntax errors
2 parents 983d0ff + 0c65ff9 commit d8b98cd

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
@@ -101,7 +101,6 @@ process {
101101
// Read QC and trimming options
102102
//
103103

104-
if (!(params.skip_fastqc || params.skip_qc)) {
105104
process {
106105
withName: 'FASTQC' {
107106
ext.args = '--quiet'
@@ -119,9 +118,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
119118
]
120119
}
121120
}
122-
}
123121

124-
if (!params.skip_trimming) {
125122
process {
126123
withName: 'TRIMGALORE' {
127124
ext.args = {
@@ -159,7 +156,6 @@ if (!params.skip_trimming) {
159156
]
160157
}
161158
}
162-
}
163159

164160
process {
165161
withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
@@ -192,7 +188,6 @@ process {
192188
}
193189
}
194190

195-
if (params.aligner == 'bwa') {
196191
process {
197192
withName: 'BWA_MEM' {
198193
ext.args = {
@@ -212,9 +207,7 @@ if (params.aligner == 'bwa') {
212207
]
213208
}
214209
}
215-
}
216210

217-
if (params.aligner == 'bowtie2') {
218211
process {
219212
withName: 'BOWTIE2_ALIGN' {
220213
ext.args = {
@@ -240,9 +233,7 @@ if (params.aligner == 'bowtie2') {
240233
]
241234
}
242235
}
243-
}
244236

245-
if (params.aligner == 'chromap') {
246237
process {
247238
withName: 'CHROMAP_INDEX' {
248239
publishDir = [
@@ -264,9 +255,7 @@ if (params.aligner == 'chromap') {
264255
]
265256
}
266257
}
267-
}
268258

269-
if (params.aligner == 'star') {
270259
process {
271260
withName: '.*:ALIGN_STAR:STAR_ALIGN' {
272261
ext.args = [
@@ -300,7 +289,6 @@ if (params.aligner == 'star') {
300289
]
301290
}
302291
}
303-
}
304292

305293
process {
306294
withName: 'PICARD_MERGESAMFILES' {
@@ -480,7 +468,6 @@ process {
480468
}
481469
}
482470

483-
if (!params.skip_picard_metrics) {
484471
process {
485472
withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
486473
ext.args = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
@@ -499,9 +486,7 @@ if (!params.skip_picard_metrics) {
499486
]
500487
}
501488
}
502-
}
503489

504-
if (!params.skip_preseq) {
505490
process {
506491
withName: 'PRESEQ_LCEXTRAP' {
507492
ext.args = '-verbose -bam -seed 1'
@@ -513,9 +498,7 @@ if (!params.skip_preseq) {
513498
]
514499
}
515500
}
516-
}
517501

518-
if (!params.skip_plot_profile) {
519502
process {
520503
withName: 'DEEPTOOLS_COMPUTEMATRIX' {
521504
ext.args = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
@@ -545,9 +528,7 @@ if (!params.skip_plot_profile) {
545528
]
546529
}
547530
}
548-
}
549531

550-
if (!params.skip_plot_fingerprint) {
551532
process {
552533
withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
553534
ext.args = { [
@@ -563,7 +544,6 @@ if (!params.skip_plot_fingerprint) {
563544
]
564545
}
565546
}
566-
}
567547

568548
process {
569549
withName: 'MACS3_CALLPEAK' {
@@ -599,7 +579,6 @@ process {
599579
}
600580
}
601581

602-
if (!params.skip_peak_annotation) {
603582
process {
604583
withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER:HOMER_ANNOTATEPEAKS' {
605584
ext.args = '-gid'
@@ -612,7 +591,6 @@ if (!params.skip_peak_annotation) {
612591
}
613592
}
614593

615-
if (!params.skip_peak_qc) {
616594
process {
617595
withName: 'PLOT_MACS3_QC' {
618596
ext.args = '-o ./ -p macs3_peak'
@@ -633,10 +611,7 @@ if (!params.skip_peak_annotation) {
633611
]
634612
}
635613
}
636-
}
637-
}
638614

639-
if (!params.skip_consensus_peaks) {
640615
process {
641616
withName: 'MACS3_CONSENSUS' {
642617
ext.when = { meta.multiple_groups || meta.replicates_exist }
@@ -659,7 +634,6 @@ if (!params.skip_consensus_peaks) {
659634
}
660635
}
661636

662-
if (!params.skip_peak_annotation) {
663637
process {
664638
withName: '.*:BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2:HOMER_ANNOTATEPEAKS' {
665639
ext.args = '-gid'
@@ -680,9 +654,7 @@ if (!params.skip_consensus_peaks) {
680654
]
681655
}
682656
}
683-
}
684657

685-
if (!params.skip_deseq2_qc) {
686658
process {
687659
withName: 'DESEQ2_QC' {
688660
ext.when = { meta.multiple_groups && meta.replicates_exist }
@@ -700,10 +672,7 @@ if (!params.skip_consensus_peaks) {
700672
]
701673
}
702674
}
703-
}
704-
}
705675

706-
if (!params.skip_igv) {
707676
process {
708677
withName: 'IGV' {
709678
publishDir = [
@@ -720,9 +689,7 @@ if (!params.skip_igv) {
720689
]
721690
}
722691
}
723-
}
724692

725-
if (!params.skip_multiqc) {
726693
process {
727694
withName: 'MULTIQC' {
728695
ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
@@ -733,4 +700,3 @@ if (!params.skip_multiqc) {
733700
]
734701
}
735702
}
736-
}

‎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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