Nextflow Modules
Showing module(s) with keyword "modkit"
| Module | Keywords | Description |
|---|---|---|
| nf-core/modkit/extractcalls | modkit methylation extract calls read-level modbam nanopore ont | Produce a per-read per-position table of base modification **calls** (pass/fail/filtered, with the called base) from a modBAM using the same thresholding algorithm as `modkit pileup`. Complementary to `modkit extract full`, which emits raw probabilities: `extract calls` emits the thresholded categorical decision per site per read. |
| nf-core/modkit/extractfull | modkit methylation extract read-level modbam nanopore ont | Transform the probabilities from the MM/ML tags in a modBAM into a tab-separated per-read-per-position table. Emits one row for every modified-base probability call in every read — useful for downstream custom filtering, plotting, and ML training. Optionally BGZF-compressed via `--bgzf` in `ext.args`. |