Splits a FASTA database into M chunks at protein boundaries for parallel MSFragger search.
This module splits a FASTA file into M chunks at protein boundaries using memory-mapped I/O via the split_fasta.py bin script.
It replicates get_fasta_offsets() and set_up_directories() from FragPipe's msfragger_pep_split.py for split-database search.
Each chunk is written to a numbered subdirectory under split_db/.
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Sample/experiment metadata |
| fasta | path | Protein sequence database in FASTA format |
| num_chunks | val(integer) | Number of chunks to split into (>= 1) |
| Channel | Type | Description |
|---|---|---|
| fasta_chunks | tuple(val, path) | split_db/*/*.fasta chunk files in numbered subdirectories |
| versions_python | topic: versions | Python version |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional arguments (not directly used by the bin script) |
| ext.prefix | ${meta.id} |
Prefix for naming |
community.wave.seqera.io/library/python:3.12.13--27a817c2c0890658
Used in the FRAGPIPE_SEARCH subworkflow (subworkflows/local/fragpipe_search/main.nf) to split the FASTA database for parallel MSFragger split-database search, improving performance on large databases.