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fix(xorf): adapt XORF call and cutoffs to xorf v0.2.0 #35

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Merged
alejandrogzi merged 2 commits into from
Oct 22, 2026
Merged

fix(xorf): adapt XORF call and cutoffs to xorf v0.2.0 #35

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93a473b
fix(xorf): restore 19-input XORF call for v0.2.0
alejandrogzi Oct 22, 2026
b98fb41
fix(xorf): use the v3.2 model cutoffs
alejandrogzi Oct 22, 2026
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11 changes: 9 additions & 2 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -206,11 +206,13 @@ params {
xorf_custom_database = null // custom protein db: .dmnd/.dmnd.gz replaces default; .fa/.fasta/.fa.gz appended to SwissProt and reindexed
xorf_chunk_size = 20 // chunk size for XORF parallel processing
xorf_skip_netstart = true // skip netstart
xorf_predict_min_score_max_predictions = 0.50 // min score for ORF predictions
xorf_skip_transaid = false // skip TransAID; PREDICT scores with its no-TransAID model
xorf_predict_min_score_max_predictions = -1 // negative: model bundle cutoff (0.29; 0.33 with skip_transaid)
xorf_predict_max_predictions = 3 // max ORF predictions per region
xorf_predict_threshold = 0.03 // prediction threshold
xorf_predict_threshold = -1 // negative: model bundle cutoff; only sets predicted_class
xorf_predict_keep_raw = false // keep raw predictions
xorf_do_polishing = true // polish ORFs (duplicates, truncations)
xorf_strip_truncations = true // drop predictions flagged as 5' truncations
xorf_skip_joined_concat = false // skip joined concatenation of chunks
xorf_rename_deactivate = false // disable ORF renaming
xorf_rename_rebase = false // rebase names to short hashes
Expand Down Expand Up @@ -940,6 +942,11 @@ process {
base_args = base_args + ' --keep-raw'
}

// Without TransAID scores, score with the bundled model trained without them.
if (params.xorf_skip_transaid) {
base_args = base_args + ' --no-transaid'
}

if (base_args.size() > 0) {
return base_args.join(' ')
} else {
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6 changes: 4 additions & 2 deletions params.json
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Expand Up @@ -88,11 +88,13 @@
"xorf_custom_database": null,
"xorf_chunk_size": 20,
"xorf_skip_netstart": true,
"xorf_predict_min_score_max_predictions": 0.50,
"xorf_skip_transaid": false,
"xorf_predict_min_score_max_predictions": -1,
"xorf_predict_max_predictions": 3,
"xorf_predict_threshold": 0.03,
"xorf_predict_threshold": -1,
"xorf_predict_keep_raw": false,
"xorf_do_polishing": true,
"xorf_strip_truncations": true,
"xorf_skip_joined_concat": false,
"xorf_rename_deactivate": false,
"xorf_rename_rebase": true,
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5 changes: 5 additions & 0 deletions subworkflows/xorf/main.nf
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Expand Up @@ -169,9 +169,14 @@ workflow XORF_RUN {
ch_esm_weights,
params.xorf_predict_keep_raw,
params.xorf_selenocysteine_sites,
// Keep this positional order in sync with modules/xorf/src/subworkflows/xorf/main.nf.
// v0.1.2 added skip_transaid after skip_netstart and strip_truncations after
// do_polishing; v0.2.0 keeps the same 19-input signature.
params.xorf_skip_netstart,
params.xorf_skip_transaid,
params.xorf_rename_deactivate,
params.xorf_do_polishing,
params.xorf_strip_truncations,
params.xorf_skip_joined_concat,
false, null, null, // run_only_on / run_only_mode / run_only_target — masking not ported
ch_database_versions.mix(ch_esm_versions)
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