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Merged
merged 13 commits into from
Jul 4, 2024
Merged

Update docs + database params, skip hmmsearch #391

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1632179
Add all changes mentioned in changelog
jasmezz Jul 3, 2024
d31aeb1
Remove script file (was added by mistake)
jasmezz Jul 3, 2024
2946972
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jasmezz Jul 4, 2024
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jasmezz Jul 4, 2024
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jasmezz Jul 4, 2024
7ebf74e
Merge branch 'dev' into docs-update
jasmezz Jul 4, 2024
c1ea976
Fix linting
jasmezz Jul 4, 2024
8590a74
Merge branch 'docs-update' of github.com:nf-core/funcscan into docs-u…
jasmezz Jul 4, 2024
3d3a721
Update icons, put some entries in correct order
jasmezz Jul 4, 2024
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jfy133 Jul 4, 2024
239ea4f
Fix linting
jfy133 Jul 4, 2024
67c9f6a
Fix HMMSearch variables in text reporintg
jfy133 Jul 4, 2024
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Final changes
jfy133 Jul 4, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -28,7 +28,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#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)
- [#391](https://github.com/nf-core/funcscan/pull/391) Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated all "database" parameters, updated docs. (by @jasmezz)
- [#391](https://github.com/nf-core/funcscan/pull/391) Skip hmmmsearch by default to not crash pipeline if user provides no HMM files, updated docs. (by @jasmezz)
- [#391](https://github.com/nf-core/funcscan/pull/391) Unified all "database" parameters. (by @jasmezz)

### `Dependencies`

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2 changes: 1 addition & 1 deletion docs/usage.md
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Expand Up @@ -162,7 +162,7 @@ This requires supplying a list of HMM files ending in `.hmm`, that have models f
You should place all HMMs in a directory, supply them to the AMP or BGC workflow and switch hmmsearch on like:

```bash
--amp_run_hmmsearch --amp_hmmsearch_models '/<path>/<to>/<amp>/*.hmm'
--amp_run_hmmsearch --amp_hmmsearch_models "/<path>/<to>/<amp>/*.hmm"
```

### AMPcombi
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -207,7 +207,7 @@ params {
bgc_antismash_taxon = 'bacteria'

bgc_skip_deepbgc = false
bgc_deepbgc_db = null
bgc_deepbgc_db = null
bgc_deepbgc_score = 0.5
bgc_deepbgc_prodigalsinglemode = false
bgc_deepbgc_mergemaxproteingap = 0
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2 changes: 1 addition & 1 deletion subworkflows/local/utils_nfcore_funcscan_pipeline/main.nf
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Expand Up @@ -236,7 +236,7 @@ def toolCitationText() {
!params.bgc_skip_antismash ? "antiSMASH (Blin et al. 2021)," : "",
!params.bgc_skip_deepbgc ? "deepBGC (Hannigan et al. 2019)," : "",
!params.bgc_skip_gecco ? "GECCO (Carroll et al. 2021)," : "",
params.amp_run_hmmsearch ? "HMMER (Eddy 2011)," : "",
params.bgc_run_hmmsearch ? "HMMER (Eddy 2011)," : "",
". The output from the biosynthetic gene cluster screening tools were standardised and summarised with comBGC (Frangenberg et al. 2023)."
].join(' ').replaceAll(", +\\.", ".").trim()

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