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Merged
pinin4fjords merged 1 commit into from
Dec 5, 2025
+31 −21
Merged

fix(anota2seq): add gene IDs and handle empty results #9510

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10 changes: 5 additions & 5 deletions modules/nf-core/anota2seq/anota2seqrun/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ process ANOTA2SEQ_ANOTA2SEQRUN {
tuple val(meta2), path(samplesheet), path(counts)

output:
tuple val(meta), path("*.translated_mRNA.anota2seq.results.tsv") , emit: translated_mrna
tuple val(meta), path("*.total_mRNA.anota2seq.results.tsv") , emit: total_mrna
tuple val(meta), path("*.translation.anota2seq.results.tsv") , emit: translation
tuple val(meta), path("*.buffering.anota2seq.results.tsv") , emit: buffering
tuple val(meta), path("*.mRNA_abundance.anota2seq.results.tsv") , emit: mrna_abundance
tuple val(meta), path("*.translated_mRNA.anota2seq.results.tsv") , emit: translated_mrna, optional: true
tuple val(meta), path("*.total_mRNA.anota2seq.results.tsv") , emit: total_mrna, optional: true
tuple val(meta), path("*.translation.anota2seq.results.tsv") , emit: translation, optional: true
tuple val(meta), path("*.buffering.anota2seq.results.tsv") , emit: buffering, optional: true
tuple val(meta), path("*.mRNA_abundance.anota2seq.results.tsv") , emit: mrna_abundance, optional: true
tuple val(meta), path("*.Anota2seqDataSet.rds") , emit: rdata
tuple val(meta), path("*.fold_change.png") , emit: fold_change_plot
tuple val(meta), path("*.interaction_p_distribution.pdf") , emit: interaction_p_distribution_plot , optional: true
Expand Down
26 changes: 18 additions & 8 deletions modules/nf-core/anota2seq/anota2seqrun/templates/anota2seqrun.r
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Expand Up @@ -116,6 +116,7 @@ opt <- list(
reference_level = '$reference',
target_level = '$target',
sample_id_col = "sample",
gene_id_col = "gene_id",
samples_pairing_col = NULL,
samples_batch_col = NULL,
subset_to_contrast_samples = FALSE,
Expand Down Expand Up @@ -366,14 +367,23 @@ for (analysis in c("translated mRNA", "total mRNA", "translation", "buffering",
selContrast = 1
)

write.table(
output,
file = paste(opt\$output_prefix, sub(' ', '_', analysis), 'anota2seq.results.tsv', sep = '.'),
col.names = TRUE,
row.names = FALSE,
sep = '\t',
quote = FALSE
)
# Only write file if there are results
if (!is.null(output) && nrow(output) > 0) {
# Add gene IDs as the first column
output_with_genes <- cbind(
setNames(data.frame(rownames(output)), opt\$gene_id_col),
output
)

write.table(
output_with_genes,
file = paste(opt\$output_prefix, sub(' ', '_', analysis), 'anota2seq.results.tsv', sep = '.'),
col.names = TRUE,
row.names = FALSE,
sep = '\t',
quote = FALSE
)
}
}

# Fold change plot
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test
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Expand Up @@ -38,7 +38,7 @@ nextflow_process {
process.out.translated_mrna,
process.out.total_mrna,
process.out.translation,
process.out.mrna_abundance,
process.out.buffering,
process.out.versions,
file(process.out.fold_change_plot[0][1]).name,
file(process.out.interaction_p_distribution_plot[0][1]).name,
Expand Down
14 changes: 7 additions & 7 deletions modules/nf-core/anota2seq/anota2seqrun/tests/main.nf.test.snap
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Expand Up @@ -6,31 +6,31 @@
{
"id": "treatment_vs_control"
},
"treatment_vs_control.translated_mRNA.anota2seq.results.tsv:md5,2c8a7dc1841d2852fc68e5d65e89a8e1"
"treatment_vs_control.translated_mRNA.anota2seq.results.tsv:md5,e777e335d484831520e53c51db75a47c"
]
],
[
[
{
"id": "treatment_vs_control"
},
"treatment_vs_control.total_mRNA.anota2seq.results.tsv:md5,69778181d0ec4f50c11c99dfed7e9090"
"treatment_vs_control.total_mRNA.anota2seq.results.tsv:md5,ea8044585fcbf133b284e7a96bf2a4a8"
]
],
[
[
{
"id": "treatment_vs_control"
},
"treatment_vs_control.translation.anota2seq.results.tsv:md5,28dca3b6017569e8a8a0702714e7451c"
"treatment_vs_control.translation.anota2seq.results.tsv:md5,99045a6fca60386e8cb5a31a49491688"
]
],
[
[
{
"id": "treatment_vs_control"
},
"treatment_vs_control.mRNA_abundance.anota2seq.results.tsv:md5,68b329da9893e34099c7d8ad5cb9c940"
"treatment_vs_control.buffering.anota2seq.results.tsv:md5,d900d02201c6703aba62cd30a10d2ded"
]
],
[
Expand All @@ -52,9 +52,9 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.2"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-06-01T14:34:20.085223495"
"timestamp": "2025-12-05T12:21:54.259548595"
}
}
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