Replicates FragPipe's database decoy check (FragpipeRun.checkDbConfig).
FragPipe checks the database before PeptideProphet, Percolator or the Philosopher filter runs.
It counts the FASTA entries whose first header field starts with the workflow decoy tag (database.decoy-tag).
In headless mode FragPipe refuses to run when the decoy share is 0, 100 %, or outside 40-60 %.
Databases of 1 GiB or more are not inspected (TabDatabase.databaseSizeLimit).
This module applies the same rule and fails with FragPipe's messages.
FRAGPIPE_DATABASE runs it on every database: --database as given, the --add_philosopher_decoy / --add_philosopher_contaminants output, and the headless path.
| Condition |
Error message |
| No FASTA entries |
Database looks to be empty |
| 0 % entries with the tag |
No decoys found in the FASTA file. |
| 100 % entries with the tag |
All FASTA entries seem to be decoys. |
| Below 40 % or above 60 % |
FASTA file contains <pct> decoys. |
| Channel |
Type |
Description |
| meta |
val(map) |
Database metadata |
| fasta |
path |
Protein database in FASTA format |
| decoy_tag |
val(string) |
Decoy protein prefix from the workflow database.decoy-tag (via getDecoyTag()) |
| Channel |
Type |
Description |
| fasta |
tuple(val, path) |
The input database, unchanged, when it passes the check |
| versions_python |
topic: versions |
Python version |
| Parameter |
Default |
Description |
| ext.args |
'' |
Additional arguments for check_db_config.py |
community.wave.seqera.io/library/python:3.12.13--27a817c2c0890658
FragpipeRun.java:2703-2765 (checkDbConfig)TabDatabase.java:79, 278-285 (size limit, decoy counting)FastaUtils.java:44-85 (getDecoysCnt, readFasta)