Vembrane filter #9340
Vembrane filter #9340
Conversation
|
Hi @famosab, This PR is originates from PR #9290, which was done using a company git account. The new PR #9340 is now from a personal account. All previous comments can be viewed in this URL. In this PR, I have added the following changes:
Please let me know if there are more changes to be made for this PR to be merge-able :) ! Cheers, |
There was a problem hiding this comment.
Hi @dhtt, we bump versions on separate PRs with renovate, so this file shouldn't be modified here
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out |
There was a problem hiding this comment.
| process.out | |
| process.out, | |
| path(process.out.versions[0]).yaml |
There was a problem hiding this comment.
Can you run nextflow lint on this :)
| vembrane filter \\ | ||
| ${args} \\ | ||
| ${expression} \\ | ||
| -o ${prefix}.filtered.vcf \\ |
There was a problem hiding this comment.
In nf-core we prefer to let the user of the module handle the output name. So we rather make them check that the prefix is modified,.
| -o ${prefix}.filtered.vcf \\ | |
| -o ${prefix}.vcf \\ |
also .vcf might not be correct maybe you can check the other vembrane module to see how this can be handled (as the output can be different formats).
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
|
There was a problem hiding this comment.
if ("${rds}" == "${prefix}.rds") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
something in that direction :)
| @@ -0,0 +1,63 @@ | |||
| # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json | |||
| name: "vembrane_filter" | |||
| description: write your description here | |||
github-project-automation
bot
moved this from Ready for review
to In progress
in Hackathon Barcelona October 2025
dhtt
force-pushed
the
vembrane_filter
branch
from
d579125 to
a290d09
Compare
dhtt
force-pushed
the
vembrane_filter
branch
from
a290d09 to
0c7152a
Compare
dhtt
force-pushed
the
vembrane_filter
branch
from
98c1c72 to
fcadf1b
Compare
famosab
left a comment
famosab
left a comment
There was a problem hiding this comment.
Looks good otherwise - very nice work 🚀
| val expression | ||
|
|
||
| output: | ||
| tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: filtered_variant |
There was a problem hiding this comment.
I think I would just call the output channel vcf as well (is more in line with the other modules)
| tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: filtered_variant | |
| tuple val(meta), path("*.{vcf,bcf,bcf.gz}"), emit: vcf |
| ontologies: [] | ||
|
|
||
| output: | ||
| filtered_variant: |
There was a problem hiding this comment.
| filtered_variant: | |
| vcf: |
5 participants
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda