Nextflow Modules
Showing module(s) with keyword "prepare"
| Module | Keywords | Description |
|---|---|---|
| nf-core/catpack/prepare | catpack cat prepare database profiling build | Creates a CAT_pack database based on input FASTAs |
| nf-core/rpbp/preparegenome | rpbp orf prepare genome bed riboseq | Build the per-ORF reference files that Rp-Bp's downstream scoring needs, starting from a genome FASTA and an annotation GTF. Enumerates every candidate open reading frame (ORF) in the annotation (annotated CDSs plus alternative start codons within transcript exons), records their genomic and per-exon coordinates, and labels them with the transcript and gene they belong to. Invokes Rp-Bp's `get_orfs` Python function directly, chaining the upstream helpers `gtf-to-bed12`, `extract-bed-sequences`, `extract-orf-coordinates`, `split-bed12-blocks` and `label-orfs`. Bypasses Rp-Bp's `prepare-rpbp-genome` umbrella script, which would also build `bowtie2` (rRNA filtering) and `STAR` (alignment) indices - neither is consumed by the Rp-Bp tools wrapped here, since alignment is supplied externally as a BAM. A minimal `chrName.txt` (one contig name per line) is seeded from the FASTA headers because `gtf-to-bed12` reads it via `--chr-name-file` to control output sort order. Note: emits the `*.annotated.bed.gz` filenames produced by `get_orfs` directly, rather than the `*.bed.gz`-renamed forms that the upstream umbrella `prepare-rpbp-genome` script produces. The downstream module outputs and consumers in this module set reference these names explicitly, so the two are functionally equivalent. |