Release 0.4.0 #514
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Release 0.4.0 #514
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Bump version to 0.4.0dev
Add metro map
Add metro map
Rename and add nf-test to structural variant calling
Update paraphase to compress and index VCFs within the module
Remove filter_vep, add missing SNV section and PED file information t…
Change SV multisample merging to allow for other callers
* Remove fastq QC concatenation * Fix configs * Fix outputs and tests * fix config formatting * fix schema * Fix CHANGELOG.md
Merge patch into dev
* Add Zenodo badge * Add Zenodo text
* Add CI test profiles to nf-test, and only use nf-test * Fix configs * Fix configs
* Sort output SNVs * Link to issue
* Fixed, added and updated minimap2 presets * Update CHANGELOG.md Co-authored-by: Anders Jemt <[email protected]> * prettier --------- Co-authored-by: Anders Jemt <[email protected]>
* Fix release test profile paths * Update changelog and schema
* Fix rank SVs with multiple families * use updated genmod modules * fix tests
* Update nf-core modules * fix tests * update methylation config * update test * update modules * update tests
* Add keep a changelog enforcer * changelog
* Annotate repeats per family * docs * test pdiff ci * remove stranger diff
* Refactor nallo.nf * review suggestions
* Annotate and rank SNVs per family * Update CHANGELOG again * remove mistakenly added file * Update output.md * Update subworkflows/local/short_variant_calling/main.nf Co-authored-by: Lucía Peña-Pérez <[email protected]> --------- Co-authored-by: Lucía Peña-Pérez <[email protected]>
* rename parameters * formatting * fix files * Update CHANGELOG.md Co-authored-by: Daniel Schmitz <[email protected]> * Update CHANGELOG.md Co-authored-by: Daniel Schmitz <[email protected]> * review suggestions * fix CHANGELOG * Update nextflow.config Co-authored-by: Daniel Schmitz <[email protected]> * Update nextflow.config Co-authored-by: Daniel Schmitz <[email protected]> * Update nextflow.config Co-authored-by: Daniel Schmitz <[email protected]> --------- Co-authored-by: Daniel Schmitz <[email protected]>
* Filter variants * CHANGELOG * Update CHANGELOG.md * Update assets/schema_hgnc_ids.json * Update subworkflows/local/filter_variants/main.nf Co-authored-by: Daniel Schmitz <[email protected]> * merge and review suggestions * review suggestions * Update subworkflows/local/filter_variants/main.nf Co-authored-by: Anders Jemt <[email protected]> * Review suggestions --------- Co-authored-by: Daniel Schmitz <[email protected]> Co-authored-by: Anders Jemt <[email protected]>
* update docs * prettier * update params * prettier * parameters * changelog
* Update nallo.nf * changelog
* Update README.md * Update CHANGELOG.md
…512) * Change missed output directory to * Change missed multi_sample output directory to family * snv to snvs * docs
* Dynamically build methods description from ch_versions * Update CONTRIBUTING.md
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Do we want to include PR #505 in the new release? |
It would be nice to update TRGT, especially since the version used in the pipeline is quite old. Previously I had some issues with using stranger with newer versions of TRGT so I'd like to do a full-sized test and upload to Scout before. I'd also like to add a repeat-caller for ONT in the coming releases, and that can't be merged by Let's see, perhaps we could do a smaller release where that PR is included. |
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Release 0.4.0 which brings:
FOUND_IN=tags in VCFsPR 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).