First Release #33
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First Release #33
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integrate divergent branches
Dev preprocessing
Updating Container Images + Improved File staging + MultiQC
bump version + cleanup + multiqc update
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Fix for failing github actions workflow
mapo9
reviewed
Nov 7, 2025
mapo9
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great work! 🚀
I was focusing on typos and code alignment a little and found a few things
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Could this error in the CI test be related to the CI Nextflow version? |
Collaborator
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I think in the past, this was more often a problem of disk space in the runner. can you try to add a clean up step before you run the pipeline? |
fix incorrect file permissions
Fixes for the release
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great work! |
luiskuhn
approved these changes
Nov 18, 2025
famosab
reviewed
Dec 12, 2025
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famosab
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Nice work!!!
A few more things and then you got the first release 🥳
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This does not exist yet? :) But I think for a first release having a full_size test profile would be nice. The full_size test does not need to run in the CI just locally and then on AWS and is what is being displayed then on the website.
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| // stage input files into the working directory | ||
| // if test profile then first data needs to be unzipped |
Contributor
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You could also do that by checking the file extension. See https://github.com/nf-core/variantprioritization/blob/dev/subworkflows/local/reference_data/main.nf how I did it. But thats just a suggestion not something you need to do :)
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oh but that's a very nice idea :)!
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## v1.0dev - [date] | ||
| ## v1.0.0 - [date] |
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Date and a release name are missing :)
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| // Load nf-core/lsmquant custom profiles from different institutions. | ||
| // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs |
Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
Member
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.3.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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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).