Nextflow Modules
Showing module(s) with keyword "catalogue"
| Module | Keywords | Description |
|---|---|---|
| nf-core/custom/orfmerge | orf ribo-seq catalogue merge clustering | Cluster normalised per-sample, per-caller ORF predictions into a single cohort-level catalogue. Pair with `custom/orfnormalise` upstream and (typically) `bedtools/getfasta` + `seqkit/translate` downstream to obtain the AA FASTA. Strategy is class-aware (operating on the harmonised `orf_class` written by `custom/orfnormalise`): - canonical_cds: collapse by (transcript_id, strand). One canonical CDS per transcript by definition. - uORF, dORF, other: collapse by (transcript_id, strand, start, end). A single transcript can host multiple distinct uORFs / dORFs / internal ORFs, so keying on the outer span keeps them in separate clusters while still merging cross-caller calls that agree on coordinates. - novel_u, smORF: greedy reciprocal-overlap clustering on the outer genomic span at `--reciprocal-overlap` (default 0.8). Catches fuzzy cross-caller matches and exact-coordinate collapses in one pass. Order-dependent at the boundary: a chain A-B-C where A-B and B-C overlap at ~0.85 but A-C only at ~0.75 may cluster as {A,B,C} or {A,B}+{C} depending on iteration order. Rare in practice at 0.8. Cross-caller consensus is recorded in two column families on the catalogue TSV: - `called_by_<caller>`: 0/1 indicator per supported caller (ribotish, ribocode, ribotricer, rpbp, price). - `score_<caller>`: best score from that caller within the cluster. Score direction is per-caller (p-values are minimised; Bayes factors / phase scores are maximised). Cross-sample recurrence is recorded in two further columns: - `n_samples`: number of distinct samples contributing to the cluster (a cohort recurrence metric). - `samples`: sorted, comma-separated list of those sample ids. Emits a small MultiQC custom-content TSV (per-class counts) for inclusion in downstream MultiQC reports. |