FragPipe's database update (CmdDatabaseUpdate), run only with --add_philosopher_decoy / --add_philosopher_contaminants.
FragPipe headless searches the workflow's database.db-path as given, so by default the pipeline does not run this module.
With --add_philosopher_decoy / --add_philosopher_contaminants it runs FragPipe's "Add decoys" argv, philosopher database --custom <fasta> [--nodecoys] [--contam --contamprefix] (CmdDatabaseUpdate.java:44-53), inside a Philosopher workspace.
There is no --prefix, so Philosopher writes its default rev_ decoys; CHECKDBCONFIG then rejects the database when the workflow decoy tag is not rev_, as FragPipe does.
With --custom, Philosopher adds the cRAP contaminants without a contam_ prefix (that tag only applies to proteome-ID downloads).
| Channel | Type | Description |
|---|---|---|
| meta | val(map) | Database metadata |
| fasta | path | Target protein FASTA file |
| Channel | Type | Description |
|---|---|---|
| fasta | tuple(val, path) | ${prefix}_philosopher.fasta database with decoys/contaminants added |
| log | tuple(val, path) | philosopher_database.log: command line, then the tool output |
| versions_philosopher | topic: versions | Philosopher version |
| versions_fragpipe | topic: versions | FragPipe version |
| Parameter | Default (conf/modules.config) |
Description |
|---|---|---|
| ext.args | from the two params (--nodecoys, --contam --contamprefix) |
Arguments after database --custom <fasta> |
| ext.prefix | ${meta.id} |
Output file prefix |
| ext.fragpipe_tools_dir | /fragpipe_bin/fragpipe-24.0/fragpipe-24.0/tools |
FragPipe tools directory for Philosopher binary discovery |
The licensed FragPipe image given with --fragpipe_container.