Release PR: dev to master

[chaochaowong]

pacvar 1.1.0, Kākāpō Awakens, expands the WGS workflow with new copy number variant (hificnv), structural variant (sawfish), 5mC methylation (pb-CpG-tools), Fiber-seq 6mA preprocessing (fibertools), and variant annotation (Ensembl VEP) capabilities. This release also updates the pipeline template to nf-core/tools 4.0.2 and refreshes core nf-core modules and infrastructure.

Notes:

• skip_fiberseq=true by default because most PacBio long-read WGS datasets are generally not using the Fiber-seq protocol for N6-methyladenosine (m6A) detection. Fiber-seq is mainly relevant for epigenetic or chromatin-focused studies.
• I am not updating the most current hiphase (v1.6.0) module in this PR because doing so would require changes to the pipeline flow and would involve substantial additional work.

Future work for v1.2.0:

• Update the hiphase module to v1.6.0 to support both SNV and SV inputs for haplotype phasing.
• Add support for Ensembl VEP --plugin and --custom options.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• If necessary, also make a PR on the nf-core/pacvar branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[SPPearce]

Generally fine, some comments (not blocking):
The use of meta.file_name in the publish paths seems weird, why are you doing that rather than just using meta.id (and only on a few outputs?).
Would be nice to finish swapping the remaining modules to use topics rather than the versions.yml.

[chaochaowong]

Generally fine, some comments (not blocking): The use of meta.file_name in the publish paths seems weird, why are you doing that rather than just using meta.id (and only on a few outputs?). Would be nice to finish swapping the remaining modules to use topics rather than the versions.yml.

First of all, thank you for reviewing this release PR.

Yes, I believe you are referring to these two publish path prefixes in modules.config:

    withName: 'HIFICNV' {
        ext.prefix = {"${meta.file_name}.cnv"}
    }

    withName: 'PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES' {
        ext.prefix = {"${meta.file_name}.cpgscores"}
    }

The reason for using meta.file_name instead of meta.id is that meta.file_name (input BAM's filename) preserves the history of how the input BAM was created. In this pipeline, users can optionally skip SNV calling and/or haplotype phasing. If we use only meta.id, the published output name would not indicate whether the input BAM had gone through those steps.

For example, if meta.id is JR26_sarcoma and the workflow includes SNV calling and HiPhase, meta.file_name becomes JR26_sarcoma.snv.phased. Therefore, the HiFiCNV output prefix becomes JR26_sarcoma.snv.phased.cnv, instead of simply JR26_sarcoma.cnv. This makes it clearer that the CNV output was generated from a BAM that had been processed with SNV calling and haplotype phasing. Same reason applies to pb-CpG-tools::alignedbamtocpgscores().

Second, I agree that it would be better to finish migrating the remaining modules to use topic channels instead of versions.yml. Because this release PR already contains a large number of commits and file changes, I would prefer to defer the remaining topic channel migration to the next release, v1.2.0 (#58). I also plan to update the HiPhase module in that release, which will require more substantial changes to the pipeline flow (#59).

Thanks again for the thoughtful review and helpful suggestions. I appreciate you taking the time to look through such a large release PR.