Update pairtools to 1.1.3 and migrating to topic version

[birkiy]

• Updated the pairtools version to 1.1.3.
• Migrated to topic versions.

[Copilot]

Pull request overview

This PR updates the nf-core pairtools module suite to the new Pairtools release and migrates software version reporting from a versions.yml file to the newer topic-based versions tuple output.

Changes:

• Bump Pairtools across modules to 1.1.3 (conda + container tags).
• Replace versions.yml generation with topic: versions tuple outputs (e.g. versions_pairtools).
• Update nf-test snapshots and assertions to match the new versions output structure.

Reviewed changes

Copilot reviewed 44 out of 44 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
modules/nf-core/pairtools/stats/main.nf	Bumps container and migrates versions output to topic-based tuple.
modules/nf-core/pairtools/stats/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/stats/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/stats/tests/main.nf.test.snap	Updates snapshot for new output + versions tuple + tool versions.
modules/nf-core/pairtools/split/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/split/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/split/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/split/tests/main.nf.test	Updates test assertions to snapshot version outputs under the new naming.
modules/nf-core/pairtools/split/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/sort/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/sort/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/sort/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/sort/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/sort/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/select/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/select/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/select/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/select/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/select/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/restrict/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/restrict/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/restrict/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/restrict/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/restrict/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/parse/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/parse/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/parse/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/parse/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/parse/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/merge/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/merge/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/merge/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/merge/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/merge/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/flip/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/flip/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/flip/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/flip/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/flip/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.
modules/nf-core/pairtools/dedup/main.nf	Bumps container and migrates versions output to topic-based tuple (removes versions.yml creation).
modules/nf-core/pairtools/dedup/environment.yml	Updates conda dependency to pairtools 1.1.3.
modules/nf-core/pairtools/dedup/meta.yml	Updates licence formatting and adds topic-based versions output metadata.
modules/nf-core/pairtools/dedup/tests/main.nf.test	Updates snapshot inputs to capture new versions outputs.
modules/nf-core/pairtools/dedup/tests/main.nf.test.snap	Updates snapshot for new versions tuple output + tool versions.

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[Copilot]

The output key is "*.pairs.stat", but the documented pattern uses a different glob style ("*{.pairs.stat}") than the rest of the pairtools modules (which use "*.{pairs.stat}" / "*.{...}"). Consider aligning this pattern with the other pairtools meta.yml files for consistency and to avoid confusing downstream tooling/docs.

[SPPearce]

Has the bioconda recipe been pinned to a numpy version? As you have removed that.

[birkiy]

@SPPearce Seems that pairtools 1.1.3 works with numpy 1.26.4

Tested as below:
nf-core modules test pairtools --profile conda

Below are the test results.

Is this okay?

[SPPearce]

The recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pairtools/meta.yaml doesn't pin a specific version of numpy, so conda will likely use the most recent whenever it is run.
Whereas the docker/singularity containers will remain pinned to whatever version that they have inside them currently.
Over time, this can lead to a drift in the numerical output, which is likely why they were pinned previously

[birkiy]

@SPPearce The new container has pairtools 1.1.3 and numpy 1.26.4.

The bioconda recipe pairtools 1.1.3, link, pinned numpy lower than v2, and the last version before v2 is 1.26.4.

The mentioned issue has been closed; open2c/pairtools#170

Would you like me to pin numpy 1.26.4?