Nextflow Modules
Showing module(s) with keyword "offset"
| Module | Keywords | Description |
|---|---|---|
| nf-core/rpbp/getperiodiclengthsoffsets | rpbp psite offset filter riboseq | Filter the per-read-length P-site offset table down to the (length, offset) pairs that will actually drive ORF-level scoring. Drops read lengths whose metagene profile is too sparsely populated, or whose periodicity Bayes factor is too low / too uncertain, so that downstream P-site counting only uses read lengths with a clean 3-nucleotide signal. Wraps Rp-Bp's `get_periodic_lengths_and_offsets` Python helper directly. Thresholds are configured via named flags in `ext.args`: `--min-count` (default: 1000), `--min-bf-mean` (default: 5), `--max-bf-var` (default: no limit), `--min-bf-likelihood` (default: 0.5). Defaults mirror `rpbp.defaults.metagene_options`. |
| nf-core/rpbp/selectperiodicoffsets | rpbp psite offset orf riboseq | Pick the single best P-site offset for each read length from the per-(length, offset) Bayes factor table produced upstream. For each read length, the offset with the highest periodicity Bayes-factor mean is selected - this is the offset that, when added to a read's 5' end, is estimated to land closest to the ribosomal P-site (the codon being decoded). Downstream, these offsets are used to convert raw read 5'-end coordinates into P-site positions when counting reads against candidate ORFs. Emits one row per read length (length, best offset, supporting Bayes factor statistics). The next step (`rpbp/getperiodiclengthsoffsets`) filters this table to the high-quality pairs that pass user-specified count / signal thresholds before P-site counting in `rpbp/extractorfprofiles`. |