Add ampcombi 2.0.1 #427
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Add ampcombi 2.0.1 #427
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@nf-core-bot fix linting |
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Uhhh that's interesting... why don't we have any CI tests 😅 |
jfy133
requested changes
Dec 4, 2024
| # This source code is licensed under the MIT license | ||
| ######################################### | ||
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| # TITLE: Download the DRAMP database if input db empty AND and make database compatible for diamond | ||
| # TITLE: Download the reference database specified by the user. |
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Shouldn't this script be wrapped up within AMPcombi itself, e.g. ampcombi download ...?
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It is but u remember the issue with it downloading the ref. database every time for each sample? We did that to only let it run once in the pipeline. I didnt add a submodule for downloading the database, its wrapped in parse_table sub module
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Also as i wrote in the PR comment, for this PR to run as it should we still need to update the module to v2.0.1, which has a sep. PR open in modules ;)
Was wondering the same, maybe because Im pushing into your branch and not the dev ? |
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That shouldn't make s difference... But let's see once it's merged into the template update branch... Ping me for re-review once you've updated and we see what happens |
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@nf-core-bot fix linting |
jfy133
reviewed
Dec 4, 2024
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@Darcy220606 where are the ampcombi 2.0 modules themselves? Or is this just the download script
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@jfy133 the Ampcombi 2.0 modules are in a separate PR, here: nf-core/modules#7142 |
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Ah ok! Then we can wait for them to go in and then update this PR :) |
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Initial review of that just done, and back to conferencing |
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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@jfy133 All the modules are updated in the PR and the new version runs locally fine. |
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Still only thre checks?! Wtf?! |
jfy133
approved these changes
Dec 16, 2024
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Let's assume it's OK... |
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You can merge away @Darcy220606 ! |
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PR checklist
This PR is dependent on ampcombi2 module update in nf-core/modules#7142, once that is approved the version bump can be done in this PR as well. This was tested locally with manual version bump.
This PR also addresses and closes issue #423.
👽👽👽👽👽👽👽👽👽 Still TODO
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,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).