# Suggestion for getting people to review massive \`nf-core/pacvar\` PR **URL:** \ **Category:** Ask for help\ **Tags:** nf-core\ **Created:** [February 1, 2026, 5:40pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525 "2026-02-01T17:40:06Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![chaochaowong](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/chaochaowong/32/2232_2.png) [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Post date:** [February 1, 2026, 5:40pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/1 "2026-02-01T17:40:06Z")
I’ve opened a PR for the **nf-core/pacvar** pipeline on the `dev` branch: > > > \### Summary > > This is new \`dev\` version includes new features with copy number …variation calling (\`hificnv\`), PacBio’s new structural variant calling (\`sawfish\`), per-CpG methylation scores (\`pb-CpG-tools\`). The template is also compliance with \`nf-core/tool 3.5.1\`. Additional updates include new parameters and assets incorporating withe new features, updated \`nf-core\` modules, and updated local subworkflow adapting new features and topic-based \`nf-core\` modules. > > \### \*\*Added-feature specifications\*\* > > 1. \`hificnv\`: Integrated the \`hificnv\` module for copy-number variant (CNVs) calling, positioned either before or after SNVs calling depending on the \`skip\_snp\` parameter. > 2. \`sawfish\`: Integrated \`sawfish\` as an optional structural variant caller, configurable via \`sv\_caller = \['pbsv', 'sawfish'\]\`. > 3. \`pb-CpG-tools\`: Integrated the \`pbcpgtools/alignedbamcpgscores\` module for CpG methylation profiling, placed before or after \`hiphase\` based on the \`skip\_phase\` setting. > > \### Added parameters > > \- main parameters (\`nexflow.config\`) > 1. \`skip\_cnv\` to skip copy number variation calling by \`hificnv\` > 2. \`skip\_cpg\` to skip CpG methylation scoring > \- genomic parameters (\`igenome.config\`) > - \`cnv\_excluded\_regions\` bed files specifying common cnv regions; files are provided by PacBio and placed at the \`assets/sawfish\` directory. > - \`expected\_cn\` bed files specifying regions with expected copy numbers; files are provided by PacBio and placed at the \`assets/sawfish\` directory. > > \### Added assets specifications > > Added \`asssets/sawfish\` directory to include bed files from PacBio for CNVs calling by Sawfish and HiFiCNV > > \### Misc. updates > > 1. Used updated and improved PacBio-related core modules including \`pbsv\`, \`hiphase\`, \`sawfish\` using wave container > 2. Updated many \`nf-core\` modules by \`nf-core modules update\` > 3. Adopted \`nf-core/tools\` template v. 3.5.1 (merged the TEMPALTE branch from \`nf-core pipliens sync\`) and resolved all the merging conflicts > 4. Update documentation: \`CHANGELOG.md\` and \`CITATION.md\` > 5. Updated testing: \`test\_full.config\` using \`sawfish\` for SV calling > > \### TODO and in progress > > 1. Integrate \`vep\` for SNV annotation (output both tsv and vcf?) > 2. Integrate \`annotsv\` for SV annotation > 3. Update metro diagram to reflect the newly-added features > 4. Update documentation including \`USAGE.md\` for PR #41 and PR #42 > > > > \## PR checklist > > \- \[x\] This comment contains a description of changes (with reason). > \- \[x\] If you've fixed a bug or added code that should be tested, add tests! > \- \[x\] If you've added a new tool - have you followed the pipeline conventions in the \[contribution docs\](https://github.com/nf-core/pacvar/tree/master/.github/CONTRIBUTING.md) > \- \[\] If necessary, also make a PR on the nf-core/pacvar \_branch\_ on the \[nf-core/test-datasets\](https://github.com/nf-core/test-datasets) repository. > \- \[x\] Make sure your code lints (\`nf-core pipelines lint\`). > \- \[x\] Ensure the test suite passes (\`nextflow run . -profile test,docker --outdir \\`). > \- \[x\] Check for unexpected warnings in debug mode (\`nextflow run . -profile debug,test,docker --outdir \\`). > \- \[x\] Usage Documentation in \`docs/usage.md\` is updated. > \- \[x\] Output Documentation in \`docs/output.md\` is updated. > \- \[x\] \`CHANGELOG.md\` is updated. > \- \[x\] \`README.md\` is updated (including new tool citations and authors/contributors). After requesting help in the Slack `#pacvar` and `#review-request` channels, I haven’t been able to get feedback for over two weeks. I suspect the main issue may be the size of the PR. Many of the changes accumulated over time as I added new features in my fork and tried to address multiple issues at once, and I didn’t initially realize how many commits and file changes had built up. Most of the changes are related to module upgrades and compliance with the nf-core template v3.5.1. The core workflow-related changes are primarily confined to `workflow/pacvar.nf`, along with the addition of new local subworkflows to support structural variant and copy-number variant calling. I’d appreciate advice on how best to proceed. Should I continue to follow up with the lead developer, or would it be preferable to split this into multiple smaller PRs? Breaking it up would require a significant time investment (on the order of several weeks), but I’m willing to do so if that’s the recommended path forward. Any guidance would be very welcome. Thank you. Sincerely, Chao-Jen ---
**Author:** ![Evangelos\_Karatzas](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/evangelos_karatzas/32/2226_2.png) [@Evangelos\_Karatzas](https://community.seqera.io/u/Evangelos_Karatzas)\ **Post date:** [February 1, 2026, 8:23pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/2 "2026-02-01T20:23:33Z")
Describing what’s in the PR really helps, and pointing the reviewers towards the files with the main changes. In the future, aim for smaller releases, for example every time a template update is out, together with any (even small) PRs you might have until then, make a release PR. Let me have a look tomorrow morning! ---
**Author:** ![chaochaowong](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/chaochaowong/32/2232_2.png) [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Post date:** [February 2, 2026, 2:49am UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/3 "2026-02-02T02:49:18Z")
Thank you very much again. This has been a valuable learning process for me, and I truly appreciate your comments and guidance. I’ve updated the PR comments to include additional details. ---
**Author:** ![Peter\_Kneale](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/peter_kneale/32/1822_2.png) [@Peter\_Kneale](https://community.seqera.io/u/Peter_Kneale)\ **Post date:** [February 3, 2026, 1:42am UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/4 "2026-02-03T01:42:20Z")
The PR is too large to review effectively. 200 files & 76 commits. - An indication of this is that github is unable to render the PR properly (“Single file mode Due to the size of this pull request, only one file can be shown at a time.” - Another issue is that is crosses many domains, you’re unlikely to find someone who can provide constructive advice on both devcontainers, github actions, pre-commit hooks and bio informatics pipelines. Personally what i would do is: - Keep your branch as a reference - Identify a small area of functionality (say your devcontainer changes just because I see them at the top) and put them into their own small branch, newly created off of the master branch, and open a PR for just that - These can be reviewed quickly and easily - Once that PR is merged, rebase your personal reference branch on the updated master and observe that your branch now differs from master slightly less. - Its a labourous process but you’ll gradually be able to break down this monolithic PR into many small ones ---
**Author:** ![chaochaowong](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/chaochaowong/32/2232_2.png) [@chaochaowong](https://community.seqera.io/u/chaochaowong)\ **Post date:** [February 4, 2026, 11:17pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/5 "2026-02-04T23:17:56Z")
Peter\_Kneale, thank you for the valuable comments and for carefully drafting the guidance that helps keep PRs clean and easier for both developers and reviewers. I really appreciate it and learned a lot from this process. ---
**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\ **Post date:** [February 11, 2026, 11:18pm UTC](https://community.seqera.io/t/suggestion-for-getting-people-to-review-massive-nf-core-pacvar-pr/2525/6 "2026-02-11T23:18:31Z")
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