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Fix strict syntax errors #1551

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Fix strict syntax errors #1551

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3 changes: 2 additions & 1 deletion modules/local/star_align_igenomes/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,8 @@ process STAR_ALIGN_IGENOMES {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def reads1 = [], reads2 = []
def reads1 = []
def reads2 = []
meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf"
def seq_platform = seq_platform ? "'PL:$seq_platform'" : ""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/hisat2/build/main.nf
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3 changes: 2 additions & 1 deletion modules/nf-core/salmon/quant/main.nf
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18 changes: 7 additions & 11 deletions subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,6 @@
// Subworkflow with functionality specific to the nf-core/rnaseq pipeline
//

import groovy.json.JsonSlurper

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS
Expand Down Expand Up @@ -80,10 +78,6 @@ workflow PIPELINE_INITIALISATION {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

def pass_mapped_reads = [:]
def pass_trimmed_reads = [:]
def pass_strand_check = [:]

workflow PIPELINE_COMPLETION {

take:
Expand All @@ -99,6 +93,10 @@ workflow PIPELINE_COMPLETION {
strand_status // map: pass/fail status per sample for strandedness check

main:
def pass_mapped_reads = [:]
def pass_trimmed_reads = [:]
def pass_strand_check = [:]

summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
def multiqc_reports = multiqc_report.toList()

Expand All @@ -117,8 +115,6 @@ workflow PIPELINE_COMPLETION {
id, status -> pass_strand_check[id] = status
}

def multiqc_report_list = multiqc_report.toList()

//
// Completion email and summary
//
Expand All @@ -135,7 +131,7 @@ workflow PIPELINE_COMPLETION {
)
}

rnaseqSummary(monochrome_logs=monochrome_logs, pass_mapped_reads=pass_mapped_reads, pass_trimmed_reads=pass_trimmed_reads, pass_strand_check=pass_strand_check)
rnaseqSummary(monochrome_logs, pass_mapped_reads, pass_trimmed_reads, pass_strand_check)

if (hook_url) {
imNotification(summary_params, hook_url)
Expand Down Expand Up @@ -301,15 +297,15 @@ def validateInputParameters() {

// Check rRNA databases for sortmerna
if (params.remove_ribo_rna) {
ch_ribo_db = file(params.ribo_database_manifest)
def ch_ribo_db = file(params.ribo_database_manifest)
if (ch_ribo_db.isEmpty()) {
error("File provided with --ribo_database_manifest is empty: ${ch_ribo_db.getName()}!")
}
}

// Check if file with list of fastas is provided when running BBSplit
if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list) {
ch_bbsplit_fasta_list = file(params.bbsplit_fasta_list)
def ch_bbsplit_fasta_list = file(params.bbsplit_fasta_list)
if (ch_bbsplit_fasta_list.isEmpty()) {
error("File provided with --bbsplit_fasta_list is empty: ${ch_bbsplit_fasta_list.getName()}!")
}
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10 changes: 4 additions & 6 deletions subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
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2 changes: 1 addition & 1 deletion subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
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11 changes: 5 additions & 6 deletions subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
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20 changes: 10 additions & 10 deletions workflows/rnaseq/main.nf
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Expand Up @@ -69,13 +69,6 @@ include { FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS } from '../../subwor
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

// Header files for MultiQC
ch_pca_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true)
sample_status_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/sample_status_header.txt", checkIfExists: true)
ch_clustering_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true)
ch_biotypes_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/biotypes_header.txt", checkIfExists: true)
ch_dummy_file = ch_pca_header_multiqc

workflow RNASEQ {

take:
Expand All @@ -100,6 +93,13 @@ workflow RNASEQ {

main:

// Header files for MultiQC
ch_pca_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true)
sample_status_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/sample_status_header.txt", checkIfExists: true)
ch_clustering_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true)
ch_biotypes_header_multiqc = file("$projectDir/workflows/rnaseq/assets/multiqc/biotypes_header.txt", checkIfExists: true)
ch_dummy_file = ch_pca_header_multiqc

ch_multiqc_files = Channel.empty()
ch_trim_status = Channel.empty()
ch_map_status = Channel.empty()
Expand Down Expand Up @@ -545,7 +545,7 @@ workflow RNASEQ {
// Get RSeqC modules to run
def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
if (params.bam_csi_index) {
for (rseqc_module in ['read_distribution', 'inner_distance', 'tin']) {
['read_distribution', 'inner_distance', 'tin'].each { rseqc_module ->
if (rseqc_modules.contains(rseqc_module)) {
rseqc_modules.remove(rseqc_module)
}
Expand All @@ -572,12 +572,12 @@ workflow RNASEQ {
.map {
meta, strand_log ->
def rseqc_inferred_strand = getInferexperimentStrandedness(strand_log, params.stranded_threshold, params.unstranded_threshold)
rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness
def rseqc_strandedness = rseqc_inferred_strand.inferred_strandedness

def status = 'fail'
def multiqc_lines = []
if (meta.salmon_strand_analysis) {
salmon_strandedness = meta.salmon_strand_analysis.inferred_strandedness
def salmon_strandedness = meta.salmon_strand_analysis.inferred_strandedness

if (salmon_strandedness == rseqc_strandedness && rseqc_strandedness != 'undetermined') {
status = 'pass'
Expand Down
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