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fix(xorf): adapt XORF call and cutoffs to xorf v0.2.0 - #35
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xorf v0.1.2 added skip_transaid (after skip_netstart) and strip_truncations (after do_polishing) to the XORF take block. The submodule bump to v0.2.0 therefore failed before execution with 'declares 19 input channels but 17 were given'. Pass both from xasm params, defaulting to upstream behavior (skip_transaid=false, strip_truncations=true), mirror --no-transaid in PREDICT when skip_transaid is enabled, and document both in nextflow.config/params.json.
xorf v0.2.0 ships the v3.2 classifier with its cutoff in the model bundle (0.29; 0.33 for the no-TransAID model). The old 0.50 / 0.03 overrides retained fewer annotated CDSs (0.55-0.85% fewer coding transcripts upstream). Set predict_min_score_max_predictions and predict_threshold to -1 so both come from the bundle.
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Why
xorf v0.2.0 changes the
XORFtake signature from 17 to 19 inputs. xasm's wrapper still passed 17, so every run failed during workflow validation before any task ran:The two inputs were added upstream in v0.1.2:
skip_transaidafterskip_netstart, andstrip_truncationsafterdo_polishing.v0.2.0 also ships the v3.2 classifier with its cutoff in the model bundle (
0.29;0.33for the no-TransAID model). xasm still overrode it with0.50/0.03; upstream reports that keeping0.50calls 0.55-0.85% fewer coding transcripts.Changes
skip_transaidandstrip_truncationstoXORFwith upstream defaults (false/true), preserving the previous always-strip behavior.xorf_skip_transaidandxorf_strip_truncationsinnextflow.configandparams.json.--no-transaidto PREDICT whenxorf_skip_transaidis enabled, so the no-TransAID model is actually selected.xorf_predict_min_score_max_predictionsandxorf_predict_thresholdto-1so both use the model bundle cutoff.Testing
nextflow config . -profile test,dockernextflow run . -profile test,docker -preview(previously failed at theXORFinvocation with the arity error)teste2e cannot run on the local arm64 host:ghcr.io/alejandrogzi/genepred:latesthas no arm64 manifest, and amd64 emulation segfaultsdeacon. CI will exercise the full profile.Note: the
--infer_strandednesswarning in the report is unrelated.validateRun()only warns on the fastp path and does not fail the run; the fatal error was the input-channel count.