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Update deepbgc/pipeline #386

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merged 17 commits into from
Jun 21, 2024
Merged

Update deepbgc/pipeline #386

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9d5dec7
Update deebgc/pipeline module
jasmezz Jun 6, 2024
aa19d60
Update changelog
jasmezz Jun 6, 2024
fbc3061
Adding warning for missing deepbgc output, need only to add meta.id
jasmezz Jun 7, 2024
e00a968
Print warning if no hits found by BGC tools
jasmezz Jun 10, 2024
3fb1dae
Add missing if-else statements; add comments
jasmezz Jun 10, 2024
f6b792e
Alternative way of warning if no BGC hits are found
jasmezz Jun 12, 2024
291b6aa
Fix formatting
jasmezz Jun 12, 2024
a325aaf
Move ANNOTATION MQC mixing to right place
jfy133 Jun 17, 2024
c9ce4dd
Fix multiqc annotation channel, fix prepped_input, have all BGC tools…
jasmezz Jun 17, 2024
77b27c4
Merge branch 'dev' into update_deepbgc
jasmezz Jun 17, 2024
9e80d2d
Fix BGC tools input channel
jasmezz Jun 17, 2024
0b66fbd
Merge branch 'update_deepbgc' of github.com:nf-core/funcscan into upd…
jasmezz Jun 17, 2024
ddd4441
Remove ugly warning from nf-validation
jfy133 Jun 19, 2024
bfb76e8
Move multiQC file annotation mixing to the right place and fix duplic…
jfy133 Jun 19, 2024
18afe1f
Fix comBGC warning
jasmezz Jun 20, 2024
2970101
Fix warning if no BGC hits found
jasmezz Jun 20, 2024
7dafc16
Update CHANGELOG.md [skip ci]
jasmezz Jun 20, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#365](https://github.com/nf-core/funcscan/pull/365) Fixed AMRFinderPlus module and usage docs for manual database download. (by @jasmezz)
- [#371](https://github.com/nf-core/funcscan/pull/371) Fixed AMRFinderPlus parameter `arg_amrfinderplus_name`. (by @m3hdad)
- [#376](https://github.com/nf-core/funcscan/pull/376) Fixed an occasional RGI process failure when certain files not produced. (❤️ to @amizeranschi for reporting, fix by @amizeranschi & @jfy133)
- [#386](https://github.com/nf-core/funcscan/pull/386) Updated DeepBGC module to fix output file names, separate annotation step for all BGC tools, add warning if no BGCs found, fix MultiQC reporting of annotation workflow. (by @jfy133, @jasmezz)

### `Dependencies`

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -87,7 +87,7 @@
},
"deepbgc/pipeline": {
"branch": "master",
"git_sha": "f315f85d9ac6c321f6e3596493fd61019340df2a",
"git_sha": "0ea330bfd93fbbe5b5cae9afab565c73cc508583",
"installed_by": ["modules"]
},
"fargene": {
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50 changes: 39 additions & 11 deletions modules/nf-core/deepbgc/pipeline/main.nf
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116 changes: 116 additions & 0 deletions modules/nf-core/deepbgc/pipeline/tests/main.nf.test
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