Udate GATK modules - Fix output line lack of specificity#1839
Udate GATK modules - Fix output line lack of specificity#1839johnoooh wants to merge 12 commits intonf-core:devfrom
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@johnoooh, sorry to bother you about it, can you try using pre-commit, so that the linting stays the same on the modules.json file? |
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Since this change is also updating a version of a GATK module, I would recommend to keep this PR open, and update ALL GATK modules to the same version in just a single PR. |
maxulysse
changed the title
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Yeah I realized the module file was a pre-commit issue. I think pre-commit doesn't play nice with my HPC cluster for some reason but I'll figure that out. I'll work on the GATK versions as well, no worries! Looks like they all got the version bump a few months ago in the modules repo. |
FriederikeHanssen
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In addition, the modules should really be updated first in nf-core/modules and then secondary in nf-core.
…into bugfix/applybqsr_outfile
All of the GATK versions were bumped in the modules repo a few months ago, I'll just be using nf-core module upgrade to bring in the changes. |
Is the prefix as in all of them already? |
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Ah I thought you were referring to the version bump. The prefix issue isn’t
a problem for most modules. I’ll be fixing those in the modules repo then
np-core module updating them into sarek!
…On Mon, Mar 24, 2025 at 5:02 PM Friederike Hanssen ***@***.***> wrote:
All of the GATK versions were bumped in the modules repo a few months ago,
I'll just be using nf-core module upgrade to bring in the changes.
Is the prefix as in all of them already?
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All of the GATK versions were bumped in the modules repo a few months ago,
I'll just be using nf-core module upgrade to bring in the changes.
Is the prefix as in all of them already?
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sounds good and thanks for all the work ❤️ |
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Going to close this as it is currently being implemented in another PR |
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Addresses #1838 for the APPLYBQSR step and applies this PR from the modules repo
When using APPLYBQSR on an HPC with scratch enabled, the globbed *.bam copys both the input and output bam from scratch to the work directory. The output needed to be more specific. It is now ${prefix}.bam for the output so it now targets the output bam/cram instead of all files with the right file extension. For more details see the issue.
This should fix the issue for APPLYBQSR but be on the lookout for other modules where this occurs.
Also it looks like the modules.json is getting updated, was there a schema change? Also the gatk bioconda version is updated to 4.6.1.0
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).