Bump bcftools modules by matthdsm · Pull Request #338 · nf-cmgg/smallvariants

matthdsm · 2026-06-04T08:31:27Z

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Pull request overview

This PR updates the pipeline to use the latest nf-core bcftools module revisions, primarily standardizing VCF index outputs from separate tbi/csi channels into a single index channel and updating downstream wiring + tests accordingly. This aligns the workflow and subworkflows with the updated module interfaces and refreshes module metadata, environments, and snapshots.

Changes:

Updated multiple workflows/subworkflows to join on *.out.index instead of *.out.tbi.
Updated nf-core bcftools module definitions (main.nf, meta.yml, environment.yml) to emit a unified index output and refreshed associated nf-test snapshots/tests.
Bumped modules.json module SHAs and added a CHANGELOG.md entry for the patch release.

Reviewed changes

Copilot reviewed 55 out of 55 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
workflows/smallvariants.nf	Updates `BCFTOOLS_NORM` output join to use `out.index`.
subworkflows/local/vcf_upd_updio/main.nf	Updates `BCFTOOLS_VIEW` output join to use `out.index`.
subworkflows/local/vcf_ped_rtgtools/main.nf	Updates `BCFTOOLS_ANNOTATE` output join to use `out.index`.
subworkflows/local/vcf_filter_bcftools/main.nf	Updates `BCFTOOLS_FILTER` output join to use `out.index` (but currently mismatched with the included local module output; see comments).
subworkflows/local/vcf_concat_bcftools/main.nf	Updates `BCFTOOLS_CONCAT` output join to use `out.index`.
subworkflows/local/vcf_annotate_ensemblvep/main.nf	Updates `BCFTOOLS_SORT` output join to use `out.index` after concatenation.
modules/nf-core/bcftools/view/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/view/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/view/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/view/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/view/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/sort/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/sort/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/sort/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/sort/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/sort/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/norm/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/norm/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/norm/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/norm/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/norm/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/filter/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/filter/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/filter/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/filter/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/filter/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/concat/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/concat/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/concat/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/concat/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/concat/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/annotate/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/annotate/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/annotate/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/annotate/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/annotate/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/pluginscatter/main.nf	Collapses `tbi`/`csi` outputs into a single optional `index` output.
modules/nf-core/bcftools/pluginscatter/meta.yml	Updates outputs to `index` and reformats metadata fields.
modules/nf-core/bcftools/pluginscatter/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/pluginscatter/tests/main.nf.test	Updates nf-test assertions to use `process.out.index`.
modules/nf-core/bcftools/pluginscatter/tests/main.nf.test.snap	Updates stored snapshots to reflect `index` output structure.
modules/nf-core/bcftools/query/meta.yml	Reformats metadata fields (licence and version command typing).
modules/nf-core/bcftools/query/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/reheader/meta.yml	Reformats metadata fields (licence and version command typing).
modules/nf-core/bcftools/reheader/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules/nf-core/bcftools/stats/meta.yml	Reformats metadata fields (licence and version command typing).
modules/nf-core/bcftools/stats/environment.yml	Adds renovate hint for `bcftools` and retains `htslib` pin.
modules.json	Updates pinned nf-core module SHAs for the bcftools module set.
CHANGELOG.md	Adds `v1.13.3` entry documenting the bcftools module bump.

Comments suppressed due to low confidence (3)

subworkflows/local/vcf_concat_bcftools/main.nf:32

The emitted channel comment still documents the third tuple element as path(tbi), but this workflow now joins BCFTOOLS_CONCAT.out.index (which may be .tbi or .csi).
subworkflows/local/vcf_ped_rtgtools/main.nf:42
The emitted tuple comment still says path(tbi), but the workflow now joins on BCFTOOLS_ANNOTATE.out.index (which can be .tbi or .csi).
subworkflows/local/vcf_annotate_ensemblvep/main.nf:137
This emitted channel comment still describes the output as [ val(meta), path(vcf), path(tbi) ], but the join is now performed against BCFTOOLS_SORT.out.index (which may be .tbi or .csi).

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                    process.out.vcf,
-                    process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } },
-                    process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } },
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name } },
                    process.out.findAll { key, val -> key.startsWith("versions") }
                ).match() }


                    process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }},
-                    process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }},
-                    process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name }},
                    process.out.findAll { key, val -> key.startsWith("versions") }
                ).match() }


                    process.out.vcf.collect { it.collect { it instanceof Map ? it : file(it).name }},
-                    process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name }},
-                    process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name }},
+                    process.out.index.collect { it.collect { it instanceof Map ? it : file(it).name }},
                    process.out.findAll { key, val -> key.startsWith("versions") }
                ).match() }


@@ -63,37 +64,25 @@ output:
          description: VCF normalized output file


jhaezebr

I have no idea what I'm doing

* Bump bcftools modules (#338) * downgrade mosdepth (#336) * bump pipeline version (#339)

matthdsm added 2 commits June 4, 2026 10:26

bump bcftools module

8ae1294

fix bcftools index output

34298ed

matthdsm linked an issue Jun 4, 2026 that may be closed by this pull request

bcftools_concat fails consistently when running on nomad #337

Closed

bump changelog

6bf6d24

matthdsm changed the base branch from main to dev June 4, 2026 08:34

matthdsm requested review from ToonRosseel, Copilot and nvnieuwk June 4, 2026 08:42

Copilot started reviewing on behalf of matthdsm June 4, 2026 08:42 View session

update tests to exclude "DONE" files

9d42183

Copilot AI reviewed Jun 4, 2026

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matthdsm added 6 commits June 4, 2026 11:01

update pixi

a4d6520

drop local bcftools modules

95f4346

patch bcftools/filter

f78bf20

patch bcftools/filter

9bbf58f

patch bcftools/filter

7a21029

fix bcftools/getsamples output channel name

7c4795a

jhaezebr approved these changes Jun 4, 2026

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matthdsm merged commit 6a30339 into dev Jun 4, 2026
49 of 53 checks passed

matthdsm deleted the bump/bcftools branch June 4, 2026 11:38

matthdsm mentioned this pull request Jun 4, 2026

bcftools_concat fails consistently when running on nomad #337

Closed

matthdsm added a commit that referenced this pull request Jun 6, 2026

nf-cmgg/smallvariants v1.13.3 (#340)

ce0e506

* Bump bcftools modules (#338) * downgrade mosdepth (#336) * bump pipeline version (#339)

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Bump bcftools modules#338

Bump bcftools modules#338
matthdsm merged 10 commits into
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		@@ -63,37 +64,25 @@ output:
		description: VCF normalized output file

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matthdsm commented Jun 4, 2026

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