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Fix strict syntax errors #491

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Merged
JoseEspinosa merged 1 commit into from
Mar 19, 2026
Merged

Fix strict syntax errors #491

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34 changes: 0 additions & 34 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,6 @@ process {
// Read QC and trimming options
//

if (!(params.skip_fastqc || params.skip_qc)) {
process {
withName: 'FASTQC' {
ext.args = '--quiet'
Expand All @@ -119,9 +118,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
]
}
}
}

if (!params.skip_trimming) {
process {
withName: 'TRIMGALORE' {
ext.args = {
Expand Down Expand Up @@ -159,7 +156,6 @@ if (!params.skip_trimming) {
]
}
}
}

process {
withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
Expand Down Expand Up @@ -192,7 +188,6 @@ process {
}
}

if (params.aligner == 'bwa') {
process {
withName: 'BWA_MEM' {
ext.args = {
Expand All @@ -212,9 +207,7 @@ if (params.aligner == 'bwa') {
]
}
}
}

if (params.aligner == 'bowtie2') {
process {
withName: 'BOWTIE2_ALIGN' {
ext.args = {
Expand All @@ -240,9 +233,7 @@ if (params.aligner == 'bowtie2') {
]
}
}
}

if (params.aligner == 'chromap') {
process {
withName: 'CHROMAP_INDEX' {
publishDir = [
Expand All @@ -264,9 +255,7 @@ if (params.aligner == 'chromap') {
]
}
}
}

if (params.aligner == 'star') {
process {
withName: '.*:ALIGN_STAR:STAR_ALIGN' {
ext.args = [
Expand Down Expand Up @@ -300,7 +289,6 @@ if (params.aligner == 'star') {
]
}
}
}

process {
withName: 'PICARD_MERGESAMFILES' {
Expand Down Expand Up @@ -480,7 +468,6 @@ process {
}
}

if (!params.skip_picard_metrics) {
process {
withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
ext.args = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
Expand All @@ -499,9 +486,7 @@ if (!params.skip_picard_metrics) {
]
}
}
}

if (!params.skip_preseq) {
process {
withName: 'PRESEQ_LCEXTRAP' {
ext.args = '-verbose -bam -seed 1'
Expand All @@ -513,9 +498,7 @@ if (!params.skip_preseq) {
]
}
}
}

if (!params.skip_plot_profile) {
process {
withName: 'DEEPTOOLS_COMPUTEMATRIX' {
ext.args = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
Expand Down Expand Up @@ -545,9 +528,7 @@ if (!params.skip_plot_profile) {
]
}
}
}

if (!params.skip_plot_fingerprint) {
process {
withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
ext.args = { [
Expand All @@ -563,7 +544,6 @@ if (!params.skip_plot_fingerprint) {
]
}
}
}

process {
withName: 'MACS3_CALLPEAK' {
Expand Down Expand Up @@ -599,7 +579,6 @@ process {
}
}

if (!params.skip_peak_annotation) {
process {
withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER:HOMER_ANNOTATEPEAKS' {
ext.args = '-gid'
Expand All @@ -612,7 +591,6 @@ if (!params.skip_peak_annotation) {
}
}

if (!params.skip_peak_qc) {
process {
withName: 'PLOT_MACS3_QC' {
ext.args = '-o ./ -p macs3_peak'
Expand All @@ -633,10 +611,7 @@ if (!params.skip_peak_annotation) {
]
}
}
}
}

if (!params.skip_consensus_peaks) {
process {
withName: 'MACS3_CONSENSUS' {
ext.when = { meta.multiple_groups || meta.replicates_exist }
Expand All @@ -659,7 +634,6 @@ if (!params.skip_consensus_peaks) {
}
}

if (!params.skip_peak_annotation) {
process {
withName: '.*:BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2:HOMER_ANNOTATEPEAKS' {
ext.args = '-gid'
Expand All @@ -680,9 +654,7 @@ if (!params.skip_consensus_peaks) {
]
}
}
}

if (!params.skip_deseq2_qc) {
process {
withName: 'DESEQ2_QC' {
ext.when = { meta.multiple_groups && meta.replicates_exist }
Expand All @@ -700,10 +672,7 @@ if (!params.skip_consensus_peaks) {
]
}
}
}
}

if (!params.skip_igv) {
process {
withName: 'IGV' {
publishDir = [
Expand All @@ -720,9 +689,7 @@ if (!params.skip_igv) {
]
}
}
}

if (!params.skip_multiqc) {
process {
withName: 'MULTIQC' {
ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
Expand All @@ -733,4 +700,3 @@ if (!params.skip_multiqc) {
]
}
}
}
46 changes: 22 additions & 24 deletions workflows/chipseq.nf
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,30 +61,6 @@ include { BAM_MARKDUPLICATES_PICARD } from '../subworkflows/nf-core/bam_m
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// JSON files required by BAMTools for alignment filtering
ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)

// Header files for MultiQC
ch_spp_nsc_header = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
ch_spp_rsc_header = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
ch_spp_correlation_header = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
ch_peak_count_header = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
ch_frip_score_header = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
ch_peak_annotation_header = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
ch_deseq2_pca_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))

// Save AWS IGenomes file containing annotation version
def anno_readme = params.genomes[ params.genome ]?.readme
if (anno_readme && file(anno_readme).exists()) {
file("${params.outdir}/genome/").mkdirs()
file(anno_readme).copyTo("${params.outdir}/genome/")
}


// // Info required for completion email and summary
// def multiqc_report = []

workflow CHIPSEQ {

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

main:

// JSON files required by BAMTools for alignment filtering
ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)

// Header files for MultiQC
ch_spp_nsc_header = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
ch_spp_rsc_header = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
ch_spp_correlation_header = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
ch_peak_count_header = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
ch_frip_score_header = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
ch_peak_annotation_header = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
ch_deseq2_pca_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))

// Save AWS IGenomes file containing annotation version
def anno_readme = params.genomes[ params.genome ]?.readme
if (anno_readme && file(anno_readme).exists()) {
file("${params.outdir}/genome/").mkdirs()
file(anno_readme).copyTo("${params.outdir}/genome/")
}

ch_multiqc_files = channel.empty()

//
Expand Down
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