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famosab
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famosab
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Looks good just some minor comments :)
| file(process.out.circos[0][1]), | ||
| file(process.out.versions[0])).match() | ||
| } | ||
| { assert snapshot(process.out).match() } |
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You can use
{ assert snapshot(sanitizeOutput(process.out)).match() }
to clean up the snapshot using nft-utils. It is used to clean process and workflow outputs by removing the numbered keys. This will create snapshots that are more easy to read by humans.
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } |
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| { assert snapshot(process.out).match() } | |
| { assert snapshot(sanitizeOutput(process.out)).match() } |
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You can run
nextflow lint -format -sort-declarations -spaces 4 -harshil-alignmenton this file to clean this up nicely.
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The conda environment was broken, so I'm skipping conda tests |
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If you removed conda support then you need to add a warning that conda is not supported by this module. But I would rather try and investigate what happens with conda and why it does not work
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I looked into it and the bioconda recipe is broken. This tool requires python 2.7 (😱), but didn't pin all dependencies, so one of it (tabulate), is installed as a python3 tool, so has a broken syntax. The solution: fix the bioconda recipe by pinning all dependencies (or at least tabulate to tabulate=0.8.9)
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I see. Just updated the Bioconda recipe, waiting for its approval
| "subworkflows/nf-core/dia_proteomics_analysis", | ||
| "modules/nf-core/diann", | ||
| "modules/nf-core/doubletdetection", | ||
| "modules/nf-core/eklipse", |
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| "modules/nf-core/eklipse", |
3 participants
PR checklist
Eklipse topics migration. By some reason stub wasn't being tested, so I also added a stub test
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda