Refactor #574
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Refactor #574
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fellen31
approved these changes
Jun 26, 2024
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| - name: Run the downloaded pipeline (stub) | ||
| id: stub_run_pipeline | ||
| continue-on-error: true | ||
| env: | ||
| NXF_SINGULARITY_CACHEDIR: ./ | ||
| NXF_SINGULARITY_HOME_MOUNT: true | ||
| run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results |
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So now neither the stub run nor the regular run of the downloaded pipeline is tested? As a user of an offline cluster, it's very nice to know that nf-core download works smoothly. But if there's no space maybe there's nothing to do.
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Yeah, that's right. The downloaded pipeline is not tested anymore. I can make sure that the downloaded pipeline works locally before a release, but the github runners just don't have enough space for both the downloaded containers and the tests :(
CHANGELOG.md
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| | --------------- | ------------------------ | | ||
| | | mbuffer_mem | | ||
| | | samtools_sort_threads | | ||
| | | skip_repeat_analysis | |
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I think skip_repeat_calling would be more inline with the subworkflow name, the current output and usage docs ("Variant calling - repeat expansions"), and the parameters below.
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hmmm.. good point. The workflow includes stranger which, as you know already, is used to annotate STRs. So it does perform more than repeat calling. Perhaps I need to change the name of the subworkflow, and its references in the pipeline 😅
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I agree skip_repeat_analysis is more inline with what it actually does.
What about splitting the subworkflow into call and annotate, like you do for SNVs and SVs? Then we could use the same annotation subworkflow in both raredisease and Nallo, and you can have skip_repeat_calling and skip_repeat_annotation.
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Great minds think like 😆
That's what I am actually doing right now :D Its much easier, and like you said, it is in line with what we are doing for other variant types.
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile test_one_sample,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).