Release v1.1.0 that adds a new softmask parameter, to optionally keep original softmasking #16
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Quoted (emphasis mine) from: https://github.com/nf-core/pairgenomealign/actions/runs/11063552525/job/30739852990?pr=15 > It looks like this pull-request is has been made against the [oist/LuscombeU_nfcore_pairgenomealign_fork](https://github.com/oist/LuscombeU_nfcore_pairgenomealign_fork) `master` branch. > The `master` branch on nf-core repositories should always contain code from the latest release. > Because of this, PRs to `master` are only allowed if they come from the [oist/LuscombeU_nfcore_pairgenomealign_fork](https://github.com/oist/LuscombeU_nfcore_pairgenomealign_fork) `dev` branch. > > You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. > **Note that even after this, the test will continue to show as failing until you push a new commit.**
I always forget. That it is forbidden in nf-core pipeline to have two spaces separating two sentences.
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Co-authored-by: Matthias Hörtenhuber <[email protected]>
Release v1.1.0 that adds a new softmask parameter, to optionally keep original softmasking.
atrigila
approved these changes
Oct 9, 2024
Co-authored-by: Anabella Trigila <[email protected]>
mashehu
approved these changes
Oct 9, 2024
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This is basically the same as #15 which was just accepted, but for releasing the changes in the master branch.
By the way I need a Zenodo DOI for the pipeline and I was told on Slack that the core team needs a new release for this to happen.
I have added a new
softmaskparameter, with default value oftantanthat keeps the1.0.0pipeline behaviour. When set tooriginalthe new parameter causes the pipeline to keep the original soft-masking of the target genome instead of overriding it withtantan. No other values are accepted thanks to the nextflow schema. The patch on the schema is a bit heavy because I also grouped theseedand thesoftmaskparameter in a new group of options.There are no lint errors and I will wait for after the next nf-core tools release to address the update warnings.
PR checklist
nf-core 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).