Update all modules #1871
Update all modules #1871
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
| "preprocessing/mapped/test/test.sorted.cram", | ||
| "preprocessing/mapped/test/test.sorted.cram.crai", |
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the file name is now good <3
| # Version export | ||
| f <- file("versions.yml","w") | ||
| alleleCounter_version = system(paste("alleleCounter --version"), intern = T) | ||
| ascat_version = sessionInfo()\$otherPkgs\$ASCAT\$Version | ||
| ascat_version = as.character(packageVersion('ASCAT')) | ||
| writeLines(paste0('"', "$task.process", '"', ":"), f) | ||
| writeLines(paste(" alleleCounter:", alleleCounter_version), f) |
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We got a bunch of new tools in the environment yml. Shouldn't they be reported here?
| - bioconda::ascat=3.1.1 | ||
| - bioconda::cancerit-allelecount=4.3.0 | ||
| - bioconda::ascat=3.1.1=r42hdfd78af_0 | ||
| - bioconda::cancerit-allelecount=4.3.0=heecbde5_4 |
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Why are we adding the build ID here?
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@LouisLeNezet when you updated the module was there a reason to add this?
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I was due to conda / containers discrepancy.
| // BUG https://github.com/nf-core/modules/issues/1754 | ||
| // BUG https://github.com/bioconda/bioconda-recipes/issues/30310 | ||
| container "nf-core/deepvariant:1.6.1" | ||
| container "docker.io/google/deepvariant:1.8.0" |
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no quay.io container?
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
| - bioconda | ||
| dependencies: | ||
| # renovate: datasource=conda depName=bioconda/gatk4 | ||
| - bioconda::gatk4=4.5.0.0 |
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should we note that cnnscore variants was not upgraded and point to the deprecation notice, and request to switch to the other tool?
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
We haven't decided for the release codename yet, but I do think it will be a montain again ;-) |
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).