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fix(orftable_fasta_gtf_buildorfcatalogue): keep meta.id as the true sample id #12896

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Merged
pinin4fjords merged 5 commits into from
Sep 8, 2026
+25 −24
Merged

fix(orftable_fasta_gtf_buildorfcatalogue): keep meta.id as the true sample id #12896

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dd38dbd
fix(orftable_fasta_gtf_buildorfcatalogue): keep meta.id as the true s…
pinin4fjords Sep 6, 2026
88b829b
Merge branch 'master' into fix/orfcatalogue-caller-identity
jonasscheid Sep 7, 2026
08a8786
test: regenerate main.nf.test.snap for the meta.caller fix
pinin4fjords Sep 7, 2026
d57e89e
Merge remote (master merge + upstream CI fix) with local snapshot regen
pinin4fjords Sep 7, 2026
9144d25
refactor: drop meta.caller, reference caller directly in ext.prefix
pinin4fjords Sep 8, 2026
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14 changes: 6 additions & 8 deletions subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -32,14 +32,12 @@ workflow ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE {

// 1. Normalise each caller's output. The same module is invoked once per
// input emission; dispatch happens inside the template based on the
// `caller` val. Append the caller to meta.id so the normaliser's
// default `${meta.id}` prefix yields caller-disambiguated filenames
// (the merger stages multiple BED12s into `beds/*` and needs unique
// names per caller-sample combination).
ch_normalise_in = ch_orf_tables.map { meta, table, caller ->
[ meta + [ id: "${meta.id}.${caller}" ], table, caller ]
}
CUSTOM_ORFNORMALISE ( ch_normalise_in, ch_gtf.first() )
// `caller` val, which this subworkflow's own `ext.prefix` config also
// reads directly to disambiguate output filenames per caller (the
// merger stages multiple BED12s into `beds/*` and needs unique names
// per caller-sample combination). meta.id keeps carrying the true
// sample id through to CUSTOM_ORFNORMALISE's sample_id column.
CUSTOM_ORFNORMALISE ( ch_orf_tables, ch_gtf.first() )

// 2. Gather all normalised BED12s + sidecar TSVs across callers and
// samples into a single cohort-keyed channel. `.collect()` on an
Expand Down
3 changes: 3 additions & 0 deletions subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,4 +1,7 @@
process {
withName: '.*ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE:CUSTOM_ORFNORMALISE' {
ext.prefix = { "${meta.id}.${caller}.normalised" }
}
withName: '.*ORFTABLE_FASTA_GTF_BUILDORFCATALOGUE:BEDTOOLS_GETFASTA' {
ext.prefix = { "${meta.id}.catalogue.nt" }
ext.args = '-split -s -nameOnly'
Expand Down
32 changes: 16 additions & 16 deletions subworkflows/nf-core/orftable_fasta_gtf_buildorfcatalogue/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
{
"id": "cohort"
},
"cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"2": [
Expand Down Expand Up @@ -55,7 +55,7 @@
{
"id": "cohort"
},
"cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"7": [
Expand Down Expand Up @@ -87,7 +87,7 @@
{
"id": "cohort"
},
"cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"consensus_bed12": [
Expand All @@ -111,7 +111,7 @@
{
"id": "cohort"
},
"cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"multiqc": [
Expand All @@ -132,11 +132,11 @@
]
}
],
"timestamp": "2026-09-06T21:45:07.866746663",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
},
"timestamp": "2026-06-26T13:34:49.442717716"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"homo_sapiens [chr20] - ribotish + ribocode - collapse disabled": {
"content": [
Expand All @@ -154,7 +154,7 @@
{
"id": "cohort"
},
"cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"2": [
Expand Down Expand Up @@ -194,7 +194,7 @@
{
"id": "cohort"
},
"cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"7": [
Expand Down Expand Up @@ -226,7 +226,7 @@
{
"id": "cohort"
},
"cohort.catalogue.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"consensus_bed12": [
Expand All @@ -250,7 +250,7 @@
{
"id": "cohort"
},
"cohort.catalogue.consensus.tsv:md5,84c090458a1a96c1ba599e8ae73622e3"
"cohort.catalogue.consensus.tsv:md5,991031c264cbd81aaf4df0a18dd11ddd"
]
],
"multiqc": [
Expand All @@ -271,10 +271,10 @@
]
}
],
"timestamp": "2026-09-06T21:45:15.573125652",
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
},
"timestamp": "2026-06-26T13:34:56.775003133"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}
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