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Update modules #1180

Merged
merged 21 commits into from
Aug 17, 2023
Merged

Update modules #1180

merged 21 commits into from
Aug 17, 2023

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asp8200
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@asp8200 asp8200 commented Aug 15, 2023

For reviewers: I got into a bit of nastiness with snpeff_cache - especially in sarek.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

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Aug 15, 2023

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3b4e8bd

+| ✅ 151 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-17 08:36:55

Comment on lines +7 to +8
'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

@@ -2,7 +2,7 @@ process UNTAR {
tag "$archive"
label 'process_single'

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?

@asp8200 asp8200 marked this pull request as ready for review August 16, 2023 13:14
CHANGELOG.md Outdated Show resolved Hide resolved
CHANGELOG.md Outdated Show resolved Hide resolved
CHANGELOG.md Outdated
| `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...

modules.json Outdated Show resolved Hide resolved
asp8200 and others added 3 commits August 17, 2023 10:06
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>
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asp8200 commented Aug 17, 2023

@nf-core-bot fix linting pretty please

@asp8200 asp8200 merged commit 11c1a67 into dev Aug 17, 2023
57 checks passed
@asp8200 asp8200 deleted the update_modules branch August 17, 2023 10:13
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4 participants