Adding cellranger-arc (multiome scRNA-seq + scATAC support) #274
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Release v2.4.0
Release v2.4.1
…ign_cellrangerarc.nf and scrnaseq.nf
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… option to procide your config file
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So I move the config generation into the mkref module as suggested. Further, I added two parameters so the user can provide their own config file for cellrangerarc. Now I go to the final step and add some documentation. |
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@grst @fmalmeida @onurcanbektas I made some final changes to the subworkflows and modules. I also added some documentation to usage and output that should help. If there are not further comments, then this is finished. |
grst
reviewed
Dec 1, 2023
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Fantastic @heylf! Only still I'm still wondering is if we can merge nf-core/modules#3576 and use the central module.
We should also double-check if there weren't any last-minute changes to the local module that still need to be ported to that PR.
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| process CELLRANGERARC_COUNT { | |||
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I'll take a look if we can do something about the docker issues.
Co-authored-by: Gregor Sturm <[email protected]>
Co-authored-by: Gregor Sturm <[email protected]>
…o cellrangerarc
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@grst @fmalmeida I think I am not responsible for the lintin error? Not sure what the issue is. But modules should now also be in sync with modules in the nf-core/modules. |
Definitely not your fault! There was a very recent template update that's not yet merged into scrnaseq. We can ignore the linting here for now. |
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ok, last thing, I promise: |
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dont worr grst. Its done now |
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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).