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Update to Nextflow 25.04 #1566

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3160aac
Fix syntax errors
bentsherman May 16, 2025
407a3df
Replace version channels with topc channel
bentsherman May 16, 2025
20c3cc3
Workflow outputs [wip]
bentsherman Jun 9, 2025
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166 changes: 92 additions & 74 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,11 +9,7 @@
----------------------------------------------------------------------------------------
*/

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
GENOME PARAMETER VALUES
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
nextflow.preview.output = true

params.fasta = getGenomeAttribute('fasta')
params.additional_fasta = getGenomeAttribute('additional_fasta')
Expand All @@ -29,32 +25,25 @@ params.hisat2_index = getGenomeAttribute('hisat2')
params.salmon_index = getGenomeAttribute('salmon')
params.kallisto_index = getGenomeAttribute('kallisto')

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { RNASEQ } from './workflows/rnaseq'
include { PREPARE_GENOME } from './subworkflows/local/prepare_genome'
include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'
include { checkMaxContigSize } from './subworkflows/local/utils_nfcore_rnaseq_pipeline'

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAMED WORKFLOWS FOR PIPELINE
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
// WORKFLOW: Run main analysis pipeline
//
workflow NFCORE_RNASEQ {
workflow {

main:

ch_versions = Channel.empty()
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir
)

//
// SUBWORKFLOW: Prepare reference genome files
Expand Down Expand Up @@ -86,7 +75,6 @@ workflow NFCORE_RNASEQ {
params.skip_alignment,
params.skip_pseudo_alignment
)
ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)

// Check if contigs in genome fasta file > 512 Mbp
if (!params.skip_alignment && !params.bam_csi_index) {
Expand All @@ -96,13 +84,33 @@ workflow NFCORE_RNASEQ {
.map { checkMaxContigSize(it) }
}

ch_genome = Channel.empty().mix(
PREPARE_GENOME.out.fasta,
PREPARE_GENOME.out.gtf,
PREPARE_GENOME.out.gff,
PREPARE_GENOME.out.add_fasta,
PREPARE_GENOME.out.gene_bed,
PREPARE_GENOME.out.transcript_fasta,
PREPARE_GENOME.out.fai,
PREPARE_GENOME.out.chrom_sizes,
)

ch_genome_index = Channel.empty().mix(
PREPARE_GENOME.out.splicesites,
PREPARE_GENOME.out.bbsplit_index,
PREPARE_GENOME.out.star_index,
PREPARE_GENOME.out.rsem_index,
PREPARE_GENOME.out.hisat2_index,
PREPARE_GENOME.out.salmon_index,
PREPARE_GENOME.out.kallisto_index,
)

//
// WORKFLOW: Run nf-core/rnaseq workflow
//
ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
RNASEQ (
ch_samplesheet,
ch_versions,
PREPARE_GENOME.out.fasta,
PREPARE_GENOME.out.gtf,
PREPARE_GENOME.out.fai,
Expand All @@ -119,40 +127,6 @@ workflow NFCORE_RNASEQ {
PREPARE_GENOME.out.sortmerna_index,
PREPARE_GENOME.out.splicesites
)
ch_versions = ch_versions.mix(RNASEQ.out.versions)

emit:
trim_status = RNASEQ.out.trim_status // channel: [id, boolean]
map_status = RNASEQ.out.map_status // channel: [id, boolean]
strand_status = RNASEQ.out.strand_status // channel: [id, boolean]
multiqc_report = RNASEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
versions = ch_versions // channel: [version1, version2, ...]
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow {

main:
//
// SUBWORKFLOW: Run initialisation tasks
//
PIPELINE_INITIALISATION (
params.version,
params.validate_params,
params.monochrome_logs,
args,
params.outdir
)

//
// WORKFLOW: Run main workflow
//
NFCORE_RNASEQ ()

//
// SUBWORKFLOW: Run completion tasks
Expand All @@ -164,18 +138,68 @@ workflow {
params.outdir,
params.monochrome_logs,
params.hook_url,
NFCORE_RNASEQ.out.multiqc_report,
NFCORE_RNASEQ.out.trim_status,
NFCORE_RNASEQ.out.map_status,
NFCORE_RNASEQ.out.strand_status
RNASEQ.out.multiqc_report,
RNASEQ.out.trim_status,
RNASEQ.out.map_status,
RNASEQ.out.strand_status
)

publish:
genome = ch_genome
genome_index = ch_genome_index
star_salmon = RNASEQ.out.star_salmon
star_salmon_deseq_qc = RNASEQ.out.star_salmon_deseq_qc
star_rsem = RNASEQ.out.star_rsem
star_rsem_deseq_qc = RNASEQ.out.star_rsem_deseq_qc
hisat2 = RNASEQ.out.hisat2
multiqc_report = RNASEQ.out.multiqc_report
multiqc_data = RNASEQ.out.multiqc_data
multiqc_plots = RNASEQ.out.multiqc_plots
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FUNCTIONS
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
output {
genome {
enabled params.save_reference
path 'genome'
}

genome_index {
enabled params.save_reference
path 'genome/index'
}

star_salmon {
path 'star_salmon'
}

star_salmon_deseq_qc {
path 'star_salmon/deseq2_qc'
}

star_rsem {
path 'star_rsem'
}

star_rsem_deseq_qc {
path 'star_rsem/deseq2_qc'
}

hisat2 {
path 'hisat2'
}

multiqc_report {
path params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}"
}

multiqc_data {
path params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}"
}

multiqc_plots {
path params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}"
}
}

//
// Get attribute from genome config file e.g. fasta
Expand All @@ -189,9 +213,3 @@ def getGenomeAttribute(attribute) {
}
return null
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
THE END
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
13 changes: 2 additions & 11 deletions modules/nf-core/multiqc/main.nf
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8 changes: 0 additions & 8 deletions modules/nf-core/multiqc/nextflow.config
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9 changes: 2 additions & 7 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -142,13 +142,8 @@ params {
}

// Default publishing logic for pipeline
process {
publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
outputDir = params.outdir
workflow.output.mode = params.publish_dir_mode

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
Expand Down
6 changes: 0 additions & 6 deletions subworkflows/local/align_star/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,6 @@ workflow ALIGN_STAR {

main:

ch_versions = Channel.empty()

//
// Map reads with STAR
//
Expand All @@ -42,7 +40,6 @@ workflow ALIGN_STAR {
ch_bam_transcript = STAR_ALIGN_IGENOMES.out.bam_transcript
ch_fastq = STAR_ALIGN_IGENOMES.out.fastq
ch_tab = STAR_ALIGN_IGENOMES.out.tab
ch_versions = ch_versions.mix(STAR_ALIGN_IGENOMES.out.versions.first())
} else {
STAR_ALIGN ( reads, index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
ch_orig_bam = STAR_ALIGN.out.bam
Expand All @@ -53,14 +50,12 @@ workflow ALIGN_STAR {
ch_bam_transcript = STAR_ALIGN.out.bam_transcript
ch_fastq = STAR_ALIGN.out.fastq
ch_tab = STAR_ALIGN.out.tab
ch_versions = ch_versions.mix(STAR_ALIGN.out.versions.first())
}

//
// Sort, index BAM file and run samtools stats, flagstat and idxstats
//
BAM_SORT_STATS_SAMTOOLS ( ch_orig_bam, fasta )
ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)

emit:
orig_bam = ch_orig_bam // channel: [ val(meta), bam ]
Expand All @@ -79,5 +74,4 @@ workflow ALIGN_STAR {
flagstat = BAM_SORT_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]

versions = ch_versions // channel: [ versions.yml ]
}
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