Template update #6
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…ine sub-directories
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Added a few commits to address issues actually found in sanger-tol/ensemblgenedownload#6 and a commit to enable the |
priyanka-surana
approved these changes
Aug 9, 2023
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LGTM 👍🏼
I would recommend add the Rapid release website support only warning to the README as well.
Looking at this and gene download workflow, there seems to be a strong case for combining them. The parameters here are a subset of gene download. Most subworkflows are overlapping. And if there is still a need to keep the features apart, this can be easily done with a parameter like --download_type repeat/gene. The greatest advantage would be not having to maintain 2 very similar pipelines. It can be ensembldonwload similar to insdcdownload.
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| **sanger-tol/ensemblrepeatdownload** is a pipeline that downloads repeat annotations from Ensembl into a Tree of Life directory structure. | |||
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If the genome is non-ToL, is it still ToL directory structure?
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| **sanger-tol/ensemblrepeatdownload** is a pipeline that downloads repeat annotations from Ensembl into a Tree of Life directory structure. | |
| **sanger-tol/ensemblrepeatdownload** is a pipeline that downloads repeat annotations from Ensembl. |
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Yes. The relevant ToL directory structure for this pipeline is that the output files go into `repeats/ensembl/
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Unrelated query: What is this "Run pipeline with test data" CI that keeps running but does not complete? I saw this on |
This is one of the CI requirements we set through the pipeline website health page. Obviously we run it twice with the different version of nextflow, Github doesn't match them. We can add the version to the requirement as well, probably just the latest version? |
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I think your comments abut merging the pipelines make sense. I already have the changes regarding |
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Closes #4
I've updated the pipeline template from 2.5 to 2.8.
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).