samtools/merge: emit .bai/.crai index files by default (fixes #4261) - #12859

Merged

SPPearce merged 12 commits into

nf-core:masterfrom

ramakrishna-p21:update-samtools-merge-index

Sep 10, 2026

Commits on Sep 1, 2026

samtools/merge: emit .bai/.crai index files by default (fixes #4261)
ramakrishnapudota
committed
89abe2c
Merge remote-tracking branch 'upstream/master' into update-samtools-merge-index
ramakrishnapudota
committed
545d303

Commits on Sep 3, 2026

Merge branch 'master' into update-samtools-merge-index
ramakrishna-p21
authored
4fc9798
Refactor samtools/merge to use conditional index_format input channel
ramakrishna-p21
committed
936f62d
Merge branch 'master' into update-samtools-merge-index
ramakrishna-p21
authored
ed28b61

Commits on Sep 9, 2026

Update subworkflows/nf-core/bam_applybqsr/main.nf

ramakrishna-p21
and
SPPearce
authored
74c4b14
Update modules/nf-core/samtools/merge/meta.yml

ramakrishna-p21
and
SPPearce
authored
04d40db
Merge branch 'master' into update-samtools-merge-index
ramakrishna-p21
authored
1c60ca7
test(samtools/merge): use sanitizeOutput with readsMD5Keys and update bam_applybqsr snapshots
ramakrishna-p21
committed
ccd5280
Update modules/nf-core/samtools/merge/tests/main.nf.test

ramakrishna-p21
and
SPPearce
authored
efbdfbc
Update modules/nf-core/samtools/merge/tests/main.nf.test

ramakrishna-p21
and
SPPearce
authored
27db94f
fix(samtools/merge): restore direct fasta URL in test assertions
ramakrishna-p21
committed
5010987