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Merged
merged 7 commits into from
Feb 6, 2025
+76 −18
Merged

Prevent Pyrodigal from adding stop codon indicators #447

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0f86e9e
Add `--annotation_pyrodigal_stopcodon` parameter
jasmezz Jan 31, 2025
e76b0b4
Fix modules.config
jasmezz Jan 31, 2025
894ddeb
Fix logic of "stopcodon" param
jasmezz Feb 3, 2025
dbe492f
Fix failing snapshots
jasmezz Feb 4, 2025
d34dbf0
Merge branch 'dev' into add-pyrodigal-param
jasmezz Feb 4, 2025
19aff23
Apply suggestions from code review; fix linting warning (rocrate)
jasmezz Feb 5, 2025
5b2a679
Update description of new param
jasmezz Feb 6, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#435](https://github.com/nf-core/funcscan/pull/435) Fixed dependency errors within taxonomy merging scripts, updated the code and output for all three workflows. Bumped to version 0.1.1. (by @darcy220606)
- [#437](https://github.com/nf-core/funcscan/pull/437) Fixed file name error when supplying already preprocessed CARD database for ARG workflow. (by @jasmezz)
- [#446](https://github.com/nf-core/funcscan/pull/446) Updated antiSMASH modules to fix apptainer execution. (by @jasmezz and @jfy133)
- [#447](https://github.com/nf-core/funcscan/pull/447) Added `--annotation_pyrodigal_stopcodon` parameter to improve AMPlify screening. (by @jasmezz)

### `Dependencies`

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1 change: 1 addition & 0 deletions conf/modules.config
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Expand Up @@ -201,6 +201,7 @@ process {
params.annotation_pyrodigal_singlemode ? "-p single" : "-p meta",
params.annotation_pyrodigal_closed ? "-c" : "",
params.annotation_pyrodigal_forcenonsd ? "-n" : "",
params.annotation_pyrodigal_stopcodon ? '--no-stop-codon' : '',
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The pipeline flag should also be nostopcodon so it's clearer to the user

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Okay, is more intuitive yes. On the other hand I wanted to stick to the "codex" to have params default to false in the nextflow.config (the renamed annotation_pyrodigal_nostopcodon would have to be true by default).

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Oh I just saw that I flipped the logic by mistake 🙈 I'll update the above line to
params.annotation_pyrodigal_stopcodon ? '' : '--no-stop-codon',

"-g ${params.annotation_pyrodigal_transtable}",
].join(' ').trim()
}
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -66,6 +66,7 @@ params {
annotation_pyrodigal_closed = false
annotation_pyrodigal_transtable = 11
annotation_pyrodigal_forcenonsd = false
annotation_pyrodigal_stopcodon = false

annotation_bakta_db = null
annotation_bakta_db_downloadtype = 'full'
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7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -518,6 +518,13 @@
"fa_icon": "fas fa-barcode",
"description": "Forces Pyrodigal to scan for motifs.",
"help_text": "Forces Pyrodigal to a full scan for motifs rather than activating the Shine-Dalgarno RBS finder, the default scanner for Pyrodigal to train for motifs.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `-n`"
},
"annotation_pyrodigal_stopcodon": {
"type": "boolean",
"fa_icon": "fa fa-star-of-life",
"description": "This forces Pyrodigal to append asterisks (`*`) as stop codon indicators.",
"help_text": "Some downstream tools like AMPlify cannot process sequences containing non-sequence characters like the stop codon indicator `*`. Thus, this flag is deactivated by default. Activate this flag to revert the behaviour and have Pyrodigal append `*` as stop codon indicator to annotated sequences.\n\nFor more information check the Pyrodigal [documentation](https://pyrodigal.readthedocs.io).\n\n> Modifies tool parameter(s):\n> - PYRODIGAL: `--no-stop-codon`",
"default": false
}
},
"fa_icon": "fas fa-file-signature"
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