Comments (9)
Yes,
We have some internal nf-tests that we can start merging it here, adapting it to check only the public modules.
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e.g. https://github.com/nf-core/ampliseq/tree/dev or https://github.com/nf-core/spatialtranscriptomics, but not sure if this qualifies as "standardized".
Modules can since very recently be tested with nf-test in nf-core/modules. There's even documentation for that https://nf-co.re/docs/contributing/modules#writing-nf-test-tests
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I see, thanks! I opened one now, makes it easier to discuss...
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Hello hello,
This was merged/solved by #291
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I'm pretty sure the latest bugs in 2.5.0 would have been caught by that.
@fmalmeida, do you already have something in the internal pipeline that you could upstream here?
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Is there a nf-core pipeline already standardized with nf-test so that I can "copy" the same standards in terms of organization and setup?
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Hi @grst ,
Added the first one, for alevin aligner.
If you can take a look at that one already while I add the others, just to see if there is anything very clear that should be done different or it is fine as is.
😄
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Is there a PR I can look at 👀?
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Did not open, is still in the branch (shown in the right menu)
I can open a draft if you prefer.
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Related Issues (20)
- Universc options for BD data HOT 2
- Fix whitelist logic for Drop-seq
- Switch to use central nf-core modules
- Autorenaming of files in new cellranger module leads to erroneous renaming of sample ID containing R1 in it, like in SRR ids HOT 2
- Multi-omics support (meta-issue) HOT 1
- exceeded running time limit (8h) HOT 3
- Crash when specifying existing --star_index using star aligner HOT 2
- Bump up kb to 0.28.0 HOT 3
- Use nf-validation plugin HOT 1
- Update or remove universc HOT 8
- Tests for cellranger-arc HOT 1
- MuData conversion
- Utilize central modules for simpleaf workflow HOT 1
- The cellrangerarc cannot start successfully HOT 2
- When aligner is cellrangerarc the step MTX_TO_SEURAT failed HOT 3
- Avoid error on unknown headers in input.csv HOT 4
- Issues with samplesheet.csv as well as additional columns in the samplesheet HOT 3
- Samplesheet Check Bug HOT 1
- Flexible input read format with STARsolo with --soloBarcodeReadLength HOT 1
- Make scrnaseq pipeline v2.5.1 compatible with nextflow v22.04.0 HOT 1
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