New module: custom/collectfeaturecounts - #12846
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Collects one or more subread/featureCounts raw output files (typically one per sample, for the same feature type/ORF caller) into a single long-format table with per-sample TPM computed, dropping zero-count rows. Ported from two now-identical, independently-hardened local modules (nf-core/magmap's and nf-core/metatdenovo's own COLLECT_FEATURECOUNTS) as part of the cross-repo summary-table consolidation tracked in nf-core/magmap#237. Includes the tpm-rounding fix from nf-core/metatdenovo#483/nf-core#484 (rounds tpm to 6 decimal places, since independently-computed tpm values for the same counts can otherwise round the last significant digit differently depending on which R backend does the division). Test data (raw subread/featurecounts fixtures, real per-sample featureCounts.tsv output, not yet present on the modules branch) in nf-core/test-datasets#2247. Generated by Claude Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01UvGYU6kuXJeVv9ffdSzdzH
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August 29, 2026 07:35
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PR checklist
nf-core modules lintpasses clean.Description
Collects one or more
subread/featurecountsraw output files (typically one per sample, for the same feature type/ORF caller) into a single long-format table (orf,chr,start,end,strand,length,sample,count,tpm), computing per-sample TPM and dropping zero-count rows.Ported from two independently-hardened, now-functionally-identical local modules — nf-core/magmap's and nf-core/metatdenovo's own
COLLECT_FEATURECOUNTS— as part of a cross-repo effort to share their summary-table-generation code (tracked in nf-core/magmap#237). Both pipelines' local copies were first made caller/pipeline-agnostic by moving their one pipeline-specific ID-reconciliation special-case (magmap's genome-accession join, metatdenovo's Transdecodercds.-prefix stripping) into small local post-processing steps — see nf-core/magmap#238 and nf-core/metatdenovo#483.tpmis rounded to 6 decimal places. This carries over a fix from nf-core/metatdenovo#483/#484: when the same underlying counts get independently re-computed elsewhere (e.g. after a caller-consolidation step using a different R backend —dtplyr/data.tablehere vs plaindplyrthere), the unrounded double can round its last significant digit differently for the same mathematical value, which made an exact-equality test downstream intermittently fail. Rounding here keeps output stable regardless of which backend a consumer uses to recompute the same value.Testing
Verified with real Docker runs against two new fixtures (two samples, mixed zero/non-zero counts, one shared multi-exon gene) — nf-core/test-datasets#2247.
tpmcorrectly sums to exactly1e6per sample after rounding, zero-count rows are dropped, sample names are correctly stripped of their.sorted.bamsuffix.Generated by Claude