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?
| container "docker.io/kiranchari/varnet:latest" | ||
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| input: | ||
| tuple val(meta), path(input_normal), path(index_normal), path(input_tumor), path(index_tumor), path(intervals) |
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Tumour before normal I think makes more sense, especially as the normal is not required.
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| output: | ||
| tuple val(meta), path("${prefix}/${prefix}.vcf.gz"), emit: vcf | ||
| tuple val("${task.process}"), val("varnet"), val("1.5.0"), emit: versions_varnet, topic: versions |
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Needs the comments saying that the version is not avaialble within the container (again, if your tool, please add a way to get this)
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Fixed in the updated pull request. The version is now fetched from the container.
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Done! |
4 participants
PR checklist
Closes #XXX
topic: versions- See version_topicsnf-core modules test <MODULE> --profile docker