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Replace legacy groupTuple and transpose operators with typed groupBy and flatMap #156

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Merged
maxulysse merged 3 commits into from
Sep 24, 2026
Merged

Replace legacy groupTuple and transpose operators with typed groupBy and flatMap #156

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dbc9723
refactor: replace groupTuple and transpose with typed operators
maxulysse Sep 24, 2026
61f3be4
chore: fix CHANGELOG PR number
maxulysse Sep 24, 2026
44beddc
fix: handle single-file VCF entries in vcf flatMap
maxulysse Sep 24, 2026
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -57,6 +57,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#150](https://github.com/nf-core/references/pull/150) - Replace `branch` with `filter` + `map` in datasheet_to_channel
- [#151](https://github.com/nf-core/references/pull/151) - Enable static typing and replace `collectFile` with `WRITE_FILE`
- [#153](https://github.com/nf-core/references/pull/153) - Update modules
- [#156](https://github.com/nf-core/references/pull/156) - Replace legacy `groupTuple` and `transpose` operators with `groupBy` and `flatMap`

### Removed

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10 changes: 5 additions & 5 deletions main.nf
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Expand Up @@ -60,11 +60,11 @@ workflow NFCORE_REFERENCES {

ncbi_download_input = fasta_download_input.to_download
.mix(gff_download_input.to_download, gtf_download_input.to_download)
.map { meta, _file ->
[meta.source_version, meta.reference, meta]
}
.groupTuple()
.map { acc, ref_types, metas ->
.map { meta, _file -> [meta.source_version, [meta.reference, meta]] }
.groupBy()
.map { acc, entries ->
def ref_types = entries.collect { entry -> entry[0] }
def metas = entries.collect { entry -> entry[1] }
def includes = ref_types
.collect { reference_ ->
reference_ == 'fasta'
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2 changes: 1 addition & 1 deletion subworkflows/local/datasheet_to_channel/main.nf
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Expand Up @@ -151,7 +151,7 @@ workflow DATASHEET_TO_CHANNEL {
known_snps,
pon,
)
.transpose()
.flatMap { meta, vcfs -> vcfs instanceof Path ? [[meta, vcfs]] : vcfs.toList().collect { vcf_ -> [meta, vcf_] } }

emit:
ascat_alleles = ascat_alleles // channel: [meta, *.ascat_alleles.txt]
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2 changes: 1 addition & 1 deletion subworkflows/local/prepare_genome_rnaseq/main.nf
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Expand Up @@ -39,7 +39,7 @@ workflow PREPARE_GENOME_RNASEQ {

gtf = gtf
.mix(GFFREAD.out.gtf)
.groupTuple()
.groupBy()
.map { meta, gtf_ -> gtf_[1] ? [meta, gtf_[1]] : [meta, gtf_[0]] }

HISAT2_EXTRACTSPLICESITES(gtf.filter { meta, _gtf -> ('hisat2' in tools || 'hisat2_extractsplicesites' in tools) && meta.run_hisat2 && !hisat2_skip_splice_sites })
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