Apply multiple-testing correction to omega outputs

[Copilot]

Omega results need independent multiple-testing correction across cohort, group, and per-sample comparisons, applied separately at gene and subgenic levels, for both omega and omegagloballoc outputs.

• Multiple-testing correction pipeline

  • Added omega_multiple_testing.py to apply BH correction per {all_samples|group|sample} × {gene|subgenic} slice and emit pvalue_adj.
  • New Nextflow module OMEGA_MULTITEST runs the correction and replaces compiled omega outputs for both omega and omegagloballoc.

• Workflow wiring + outputs

  • Hooked correction into OMEGA_ANALYSIS so all_omegas*.tsv and all_omegas*_global_loc.tsv are corrected before publish.
  • Published corrected files to existing selection output paths.

• Tests/docs

  • Updated omega test expectations and README to require pvalue_adj.

Example correction behavior (BH per slice):

# pvalue_adj computed within each {cohort/group/sample} × {gene/subgenic} slice
omega_multiple_testing.py \
  --omegas-file all_omegas.tsv \
  --samples-json samples.json \
  --groups-json groups.json \
  --output all_omegas.tsv

[FerriolCalvet]

@copilot repeat the process but using the dev branch as a starting point and also open the PR for dev not for main!

[Copilot]

@FerriolCalvet I've opened a new pull request, #454, to work on those changes. Once the pull request is ready, I'll request review from you.

[FerriolCalvet]

all works well, before merging, let's discuss if the implementation is exactly the one we want to use or not.

• Decide how to deal with p-values that are set to 0.

[FerriolCalvet]

functionally tested, but missing to agree on the details of the multiple testing correction

[FerriolCalvet]

Assuming it is a float32 numeric type, we can use 1.17*10^{-38} as the minimum possible non-zero p-value.