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Prevent Pyrodigal from adding stop codon indicators #447

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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
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#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)
- [#448](https://github.com/nf-core/funcscan/pull/448) Fixed taxonomy merge to work with output from GTDB/SILVA/KALAMARI. (by @darcy220606)
- [#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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I still don't fully understand the behaviour of of this flag - a user would have to set ...stopcodon false on the CLI which is not good practise as it's not standard UNIX CLI behaviour

Suggested change
params.annotation_pyrodigal_stopcodon ? '' : '--no-stop-codon',
params.annotation_pyrodigal_usespecialstopcharacter ? '' : '--no-stop-codon',

This gives more active 'action' to the user

"-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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2 changes: 1 addition & 1 deletion tests/test.nf.test.snap
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Expand Up @@ -47,7 +47,7 @@
"deeparg_tsv_ARG": {
"content": [
"sample_1.align.daa.tsv:md5,21822364379fe8f991d27cdb52a33d1d",
"sample_2.align.daa.tsv:md5,f448465df58785a87cdee53691a77bfe",
"sample_2.align.daa.tsv:md5,d59287f357de198639bdca5dbaede173",
"sample_1.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9",
"sample_2.mapping.ARG:md5,0e049e99eab4c55666062df21707d5b9"
],
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6 changes: 3 additions & 3 deletions tests/test_preannotated.nf.test.snap
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Expand Up @@ -3,7 +3,7 @@
"content": [
"sample_1.align.daa.tsv:md5,0e71c37318bdc6cba792196d0455293d",
"sample_2.align.daa.tsv:md5,1092ecd3cd6931653168b46c7afeb9e3",
"sample_3.align.daa.tsv:md5,b79070fe26acd1a10ae3aaf06b0d5901",
"sample_3.align.daa.tsv:md5,a9ed2f0651d75b318fde07a76b06d7b8",
true,
true,
true
Expand Down Expand Up @@ -71,8 +71,8 @@
"sample_1.potential.ARG.normalized.tsv:md5,d6732b4b9765bfa47e27ba673e24b6a4",
"sample_2.ARG.normalized.tsv:md5,1a19b894a7315aaae5f799e4539e6619",
"sample_2.potential.ARG.normalized.tsv:md5,b241e22f9116d8f518ba8526d52ac4dc",
"sample_3.ARG.normalized.tsv:md5,d40d387176649ce80827420fef6a0169",
"sample_3.potential.ARG.normalized.tsv:md5,f331efd21ea143c180a15ae56a5210d3"
"sample_3.ARG.normalized.tsv:md5,d7577c0066a31e173f9cb545820650bf",
"sample_3.potential.ARG.normalized.tsv:md5,6d0889215f0ad7f601502ca67c0ca89e"
],
"meta": {
"nf-test": "0.9.0",
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