Add varnet (https://github.com/skandlab/VarNet)#11787
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| cat <<-END_VERSIONS > \$WORKDIR/versions.yml | ||
| "${task.process}": | ||
| varnet: 1.5.0 | ||
| END_VERSIONS |
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please switch to topics.
cf https://nf-co.re/blog/2025/version_topics for example
| vcf_tbi: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'sample1', single_end:false ]` | ||
| - ${prefix}/${prefix}.vcf.gz.tbi: {} |
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I feel like we're missing this in the main.nf
No tbi are being emitted out
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@maxulysse I have updated the pull request. Thank you |
The snapshots need to be updated too. They appear empty at the moment |
@maxulysse Pull requested updated. Thank you |
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
| TF_CPP_MIN_LOG_LEVEL=3 python /VarNet/filter.py \\ | ||
| --sample_name ${prefix} \\ | ||
| ${normal} \\ | ||
| --tumor_bam \$WORKDIR/${input_tumor} \\ |
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Does this really need to use WORKDIR for everything? Given it is your tool, could you patch it to respect the current working directory?
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I modified this because the test input files were using relative paths based on $WORKDIR instead of absolute paths, which was causing the tests to fail. Prepending $WORKDIR was a quick fix to make those paths valid so the tests could run.
| tag "$meta.id" | ||
| label 'process_high_memory' | ||
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| container "docker.io/kiranchari/varnet:latest" |
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Is there a plan to put it on bioconda?
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Note that a nf-core recommendation describes this: https://nf-co.re/docs/specifications/pipelines/recommendations/bioconda
We do make some exceptions for this but usually only for things like licensing issues etc. We have a #bioconda channel on slack with a bunch of experts around to help :)
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My institution requires VarNet to use a PolyForm Noncommercial License 1.0.0, which prevents adding it to bioconda. Please let me know if my understanding is incorrect.
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Never heard of that one before.
From what I can tell, it allows for redistribution, which I think would mean it is compatible with bioconda. But I'm not a bioconda expert.
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Please join the nf-core organization on GitHub to enable the CI-tests to run on your PR. You can request to join the organization via #github-invitations in the nf-core slack. You can join the nf-core slack via https://nf-co.re/join. |
Done! |
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| WORKDIR=\$(pwd) | ||
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| cd /VarNet |
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Why are you changing the directory to here? Hence you obviously need the WORKDIR.
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At the moment, my scripts rely on being in the /VarNet working directory. The test input files were using relative paths based on $WORKDIR instead of absolute paths, which was causing the tests to fail. Prepending $WORKDIR was a quick fix to make those paths valid so the tests could run.
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To be honest with you, it sounds like you need to update your tool to make it functional.
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To elaborate a little: a key feature of Nextflow is that execution of each task is encapsulated within its work directory. That way, different tasks do not affect one another and the execution becomes much safer and more reproducible.
Moving outside of the work directory violates this, and also means the pipeline is much less likely to work in diverse compute environments. eg. You typically cannot make root directories like this if you're running on a HPC using conda.
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PR checklist
Closes #XXX
topic: versions- See version_topicsnf-core modules test <MODULE> --profile docker