Update modules #1180
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Update modules #1180
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maxulysse
reviewed
Aug 15, 2023
maxulysse
reviewed
Aug 15, 2023
Comment on lines
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| 'https://depot.galaxyproject.org/singularity/cnvkit:0.9.10--pyhdfd78af_0': | ||
| 'biocontainers/cnvkit:0.9.10--pyhdfd78af_0' }" |
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why not a mulled container here?
Or maybe more, why adding samtools in this module?
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we had this before.: nf-core/modules#3651
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yeah, something weird is happening with the cnvkit modules there
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the lack of consistency is troubling me
…g of ploidy in controlfreec will be part of upcoming release.)
asp8200
commented
Aug 16, 2023
| @@ -2,7 +2,7 @@ process UNTAR { | |||
| tag "$archive" | |||
| label 'process_single' | |||
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| conda "conda-forge::sed=4.7 bioconda::grep=3.4 conda-forge::tar=1.34" | |||
| conda "conda-forge::sed=4.7 conda-forge::grep=3.11 conda-forge::tar=1.34" | |||
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@maxulysse : How would you state that update in the dependencies table?
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grep 3.4 3.11
we haven't reported channel updates
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Should the channel update be reported anywhere?
maxulysse
reviewed
Aug 17, 2023
CHANGELOG.md
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| | `tiddit` | 3.3.2 | 3.6.1 | | ||
| | Dependency | Old version | New version | | ||
| | ------------------------ | ------------------------- | ------------------------ | | ||
| | `cnvkit` | 0.9.9 (`samtools` 1.16.1) | 0.9.10 (`samtools` 1.17) | |
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not sure about specifying samtools, but it does make sense...
maxulysse
approved these changes
Aug 17, 2023
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
FriederikeHanssen
approved these changes
Aug 17, 2023
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@nf-core-bot fix linting pretty please |
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For reviewers: I got into a bit of nastiness with
snpeff_cache- especially insarek.nf. So please check that out.EDIT: Controlfreec-module not updated, since the handling of ploidy won't be part of the upcoming release of Sarek.
PR checklist
nf-core lint).nextflow run . -profile 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).