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Fix Clair3 model download staging when explicit override bypasses aut… #191

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Fix Clair3 model download staging when explicit override bypasses aut… #191

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10 changes: 8 additions & 2 deletions subworkflows/local/prepare_reference_files.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,15 @@ workflow PREPARE_REFERENCE_FILES {
// Priority: explicit meta.clair3_model param > auto-detected from BAM header via modelMap
// PacBio models from HKU mirror; ONT models from Oxford Nanopore CDN
basecall_meta.map { meta, basecall_model_meta, _kinetics_meta ->
def id_new = basecall_model_meta ? clair3_modelMap.get(basecall_model_meta) : basecall_model_meta
def meta_new = [id: id_new]
// model resolves to the samplesheet's explicit override first, falling back to the
// modelMap lookup from the auto-detected basecall model. meta_new.id reuses this same
// value (rather than recomputing it from basecall_model_meta alone) so the WGET/UNTAR
// staging directory name never diverges from the model actually being downloaded --
// previously it could resolve to null (and UNTAR would fail with "mkdir: missing
// operand") whenever basecall_model_meta didn't match the modelMap, even if an
// explicit clair3_model override was given.
def model = (!meta.clair3_model || meta.clair3_model.toString().trim() in ['', '[]']) ? clair3_modelMap.get(basecall_model_meta) : meta.clair3_model
def meta_new = [id: model]
def download_prefix = ( basecall_model_meta == 'hifi_revio' ? "https://www.bio8.cs.hku.hk/clair3/clair3_models/" : "https://cdn.oxfordnanoportal.com/software/analysis/models/clair3" )
def url = "${download_prefix}/${model}.tar.gz"
return [ meta_new, url ]
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