Dev -> Master v4.2.0 #585
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Dev -> Master v4.2.0 #585
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bump-version 4.2.0dev
Picard output is labelled as [`.intervallist`](https://github.com/nf-core/methylseq/blob/c74694ecfce6b28b877d1733e6a092bf6355ba6e/modules/nf-core/picard/bedtointervallist/main.nf#L16)
Fix error in picard_bedtointervallist.config
bump default and bismark tests after modules update 0.25.1
- Refactor version output to include process name and command used for version retrieval. - Remove legacy versions.yml file generation in favor of structured output.
- Implemented a mechanism to merge topic channel versions into the main versions file upon workflow completion. - Updated the software version output to include both main and topic versions in separate YAML files.
- Bump NFT_VER from 0.9.2 to 0.9.3 - Bump NXF_VER from 24.10.5 to 25.04.0
bwamem_index fix
… settings - Introduced new configuration for BWA_INDEX to manage reference genome output. - Added SAMTOOLS_IDXSTATS process for generating index statistics. - Updated publishDir settings in existing processes to accommodate deduplication and RRBS parameters. - Enhanced documentation to reflect new output structure and file descriptions.
… folder for --skip_deduplication and --rrbs options
Fix rrbs and skip_dedup publishing
chore: Update nf-core/methylseq to version 4.2.0
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scwatts
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Dec 9, 2025
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Congrats on the new TAPS workflow, really like the new logo too
LGTM, and I've added some very minor comments and here are a couple of notes:
- Conda support for parabricks/fq2bammeth; presumably because packing difficulties
- Rastair Conda build pinned for mbiasparser, methylkit but not mbias
I also took some time to run the test_full profile since I've never done any methylation sequence data analysis - great pipeline that works well!
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Thank you for your review @scwatts
there is no conda support for parabricks modules yet
@eduard-watchmaker could you comment on this ? |
…flow configuration, ensuring compatibility with both CPU and ARM compute environments. - apply code review suggestion
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rastair_mbias and rastair_call are tools within the original rastair suite of tools (developed by Benjamin Schuster-Boeckler) and they were the first ones to be introduced into nf-core/modules. I then added rastair_mbiasparser and rastair_methylkit to parse those outputs into other meaningful formats and implemented them in nf-core later, having to deal with other issues regarding R in the docker image / conda enviroment. If this is an issue I can make a PR to nf-core/modules to sync them up. |
fix: Added support for the `bwamem` aligner in the AWS full test work…
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Not an issue at all from my side, only drawing attention to it for awareness. I had a few other comments but they seem to have not made it into the review - I've posted one extra comment below. Similarly, only noting for awareness |
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Not very familiar with this workflow, but here's some review
| "description": "Alignment tool to use.", | ||
| "fa_icon": "fas fa-dot-circle", | ||
| "enum": ["bismark", "bismark_hisat", "bwameth"], | ||
| "enum": ["bismark", "bismark_hisat", "bwameth", "bwamem"], |
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Help text underneath needs an update?
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missed this..thanks for this....will update
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| > Daley, T., Smith, A. Predicting the molecular complexity of sequencing libraries. Nat Methods 10, 325–327 (2013). doi: [10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375) | ||
| - [rastair](https://bitbucket.org/bsblabludwig/rastair/src/master/) |
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Missing some citation string underneath?
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There is not a publication for rastair unfortunately, so no citation, just a link (and acknowledgment!) to the bitbucket repo.
| │ ├── nf_core_methylseq_software_mqc_versions.yml | ||
| │ ├── params_2024-12-13_05-36-43.json | ||
| │ └── pipeline_dag_2024-12-13_05-36-34.html | ||
| ├── rastair |
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Should this be nested inside bwamem?
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this is right. The rastair folder is outside of bwamem. plz correct me if im wrong @eduard-watchmaker
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Yes, rastair output lives outside of bwamem!
| } | ||
| .set { ch_bwamem_index_branched } | ||
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| UNTAR_BISMARK ( |
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Not a big thing, but if the others need their own UNTAR why doesn't this one?
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think it was an oversight as the generic one worked for bwamem
| ch_bwamem_inputs.fasta, | ||
| ch_bwamem_inputs.fasta_index, | ||
| ch_bwamem_inputs.bwamem_index, | ||
| params.skip_deduplication |
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Is the rrbs boolean used for other aligners not relevant here?
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rrbs is a bismark only option
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## [v4.2.0](https://github.com/nf-core/methylseq/releases/tag/4.2.0) - [2025-12-05] | ||
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Are we missing coverage of the new options? Something like:
- Added `--taps` parameter for TAPS library preset
- Added `--aligner bwamem` option for BWA-MEM alignment (recommended for TAPS)
- Added `--bwamem_index` parameter for pre-built BWA index
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these changes were bundled under the TAPS PR below
pinin4fjords
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Dec 12, 2025
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Nothing to have big concerns about
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Thank you for your time @pinin4fjords 🙏 Will for sure resolve them in the next release. |
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Thanks for the review+approval @pinin4fjords! |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).