Philosopher abacus multi-experiment report.
PHILOSOPHERABACUS mirrors FragPipe CmdPhilosopherAbacus.java:73-146.
It runs in the protXML's directory (FragPipe's work dir) on the group directories and writes combined_protein.tsv, combined_peptide.tsv and the REPRINT tables.
Abacus reads the database of the first group (Philosopher lib/aba/pro.go).
| Channel | Type | Description |
|---|---|---|
| meta, group_workspaces, group_names, protxml, combined_pepxml, abacus_cli, plex | tuple | group_workspaces: each group's .meta workspace after filter/report, in group name order; group_names: the group directory names in the same order; protxml: combined.prot.xml ([] when ProteinProphet did not run); combined_pepxml: iProphet combined.pep.xml for --peptide, else []; abacus_cli: <--picked/--uniqueonly> --razor --reprint --tag <tag> [--protein] [--peptide]; plex: TMT plex for --labels --plex <n> (0 otherwise, CmdPhilosopherAbacus.java:125-129) |
| Channel | Type | Description |
|---|---|---|
| results_dir | tuple(val, path) | Result directory |
| reprint_spc | tuple(val, path) | reprint.spc.tsv (optional) |
| reprint_int | tuple(val, path) | reprint.int.tsv (optional) |
| combined_protein | tuple(val, path) | combined_protein.tsv (optional) |
| combined_peptide | tuple(val, path) | combined_peptide.tsv (optional) |
| versions_philosopher | tuple (topic: versions) | Philosopher version |
| versions_fragpipe | tuple (topic: versions) | FragPipe version |
| Parameter | Default | Description |
|---|---|---|
| ext.args | '' | Additional CLI arguments |
| ext.prefix | meta.id | Override the output directory / file prefix |
| ext.when | (none) | Skip the process when false |
The licensed FragPipe image given with --fragpipe_container (no container is defined in the module).
Used in the FRAGPIPE_INFERENCE subworkflow (subworkflows/local/fragpipe_inference/main.nf).