CHORE: update all modules #968
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ok, let's report that all back to the github.com/nf-core/modules repo. |
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Need to update here again to get the ascat fix actually in: #702 |
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Ascat is now fixed |
| label 'process_high' | ||
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| - conda "bioconda::dragmap=1.3.0 bioconda::samtools=1.16.1 conda-forge::pigz=2.3.4" | ||
| + conda "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" |
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should we update samtools here as well, or wait for dragmap to become agreeable?
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I opened a PR over at biocontainers with updated samtools for both versions of dragmap
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Good question, I'd be happy either way
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for me we can also update all mapper / samtools combis in another PR when the biocontainers are build
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CAn you add the ascat update to the changelog, while you are at it?: https://github.com/nf-core/sarek/pull/988/files it got overlooked here |
Good catch |
maxulysse
commented
Apr 26, 2023
| @@ -1,54 +1,52 @@ | |||
| # yaml-language-server: $schema=https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json | |||
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@mashehu this is new, what it the idea behind it?
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this allows your editor to apply the schema to your meta.yml and give you hints about errors (and also what is expected for certain elements)
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I have this error in my VSCode:
Unable to parse content from 'https://github.com/nf-core/modules/tree/master/subworkflows/yaml-schema.json': Parse error at offset 7.YAML(768)
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that line is actually not in the current template, we actually point to the raw file. If you could please update this and any other occurrences of this in any meta.yml (also for modules) to: https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
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I hope I'll get a sticker for it
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nope, this is not a contribution to nf-core/infrastructure
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How come this PR is not infrastructure nf-core/modules#3306
It's a @mirpedrol / @mashehu PR
This is pure infrastructure.
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just 3 singularity tests failing, so I'm merging |
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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).