kfukuta/wf-transcriptomes-v202
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Merge branch 'em1e4' into 'dev'

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Set conv.em to 1e-4 as documented

See merge request epi2melabs/workflows/wf-transcriptomes!273
This commit is contained in:
Sam Nicholls 2026-05-19 10:04:40 +00:00
commit 56ce8d2a7e
1 changed files with 4 additions and 1 deletions
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bin/workflow_glue_r/R/bambu.R
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@ -277,7 +277,10 @@ bambu_build_args <- function(args, reads, annotation_obj, discovery, quant) {
if (quant) {
# Chunked quant re-estimates degradation bias per chunk, which changes
# the EM inputs and breaks equivalence with unchunked bambu quant.
bambu_args$opt.em <- list(degradationBias = FALSE)
# Use bambu's documented EM convergence threshold here. The looser
# implemented default (1e-2) leaves small deterministic chunk-vs-global
# quant discrepancies in the split workflow.
bambu_args$opt.em <- list(degradationBias = FALSE, conv = 1e-4)
}
bambu_args