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Adding test config with new test-datasets. See: nf-core/test-datasets#1200
Also added `publishDir` for modules
Co-authored-by: Matt Stone <matthew.stone12@gmail.com>
A sample may have multiple rows in the sample sheet, for example when data are sequenced across lanes, or across runs. Typically this is done to increase coverage as well as improve coverage uniformity (through pooling samples and splitting them across lanes/sequencers). The workflow will now process the individual lane/runs independently up through alignment of the raw reads. The aligned reads across lane/runs for a given sample will be merged prior to grouping by UMI, to ensure that reads across lanes/runs that observe the same source molecule are grouped correctly (together). The independent processing up through alignment is preferred over concatenating FASTQs as this allows for further parallelism in the processes up through alignment of raw reads.
Adds multi-lanes, single-fastq, and multi-fastq tests
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I would like to see the atomic fgbio modules being used from the nf-core modules repository, rather than the local modules here. This also includes using the most recent version (2.2.1). |
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@SPPearce how would you feel having this PR not blocked by the using the fgbio modules from nf-core, given I want to release by EOW so that I can include "We have a first release" for my talk at the Nextflow Summit later this week? I think the pipeline is functionally working, the update your proposing could be for the next minor version? |
SPPearce
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May 21, 2024
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Some feedback.
It would be nice to sync the modules up before the release, but it isn't a dealbreaker for me. Would give you the most recent version of fgbio too (although there is a mulled container to deal with, which there should be a different way to deal with soon). I have updated all the modules on the PR, if you want to take a look at that PR at some point.
The docs/output.md file is a bit light on content at the moment.
edmundmiller
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May 21, 2024
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LGTM! A few small things that could just be TODOs.
Agree with @SPPearce on those. I think an issue to track some of the things brought up from the reviews to keep track of them.
Hopefully the containers and updates will be automated soon, and there will be some motivation to move the fgbio modules to nf-core modules.
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Not sure if y'all used https://nf-co.re/docs/guidelines/graphic_design#workflow-schematics and https://nf-co.re/docs/guidelines/graphic_design#component-cheatsheets here. @jfy133 might have some words.
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Top is the description version following similar scheme
Bottom is IMO easier to read (because no tilty text, and L-T)
SVGs if you want them/tweak them etc.
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These look so much better than the really dark ones.
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Ditto, I may play around with them, thank-you!
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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SPPearce
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May 23, 2024
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
This was referenced May 23, 2024
SPPearce
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May 23, 2024
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I am going to way for the beautiful final diagrams from @jfy133 (and I'll make sure to add to the CHANGELOG with credit). But then I think we're good to go! |
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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).