Prevent Pyrodigal from adding stop codon indicators #447
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jfy133
reviewed
Feb 1, 2025
conf/modules.config
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| @@ -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',
jfy133
reviewed
Feb 5, 2025
conf/modules.config
Outdated
| @@ -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
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We need to have no stop characters appended to sequences by default, because AMPlify would ignore the whole sequence. That's the only reason for this PR. If the user prefers to have annotations with stop character for any reason (e.g. when no AMPlify is run), they can revert the default.
jfy133
approved these changes
Feb 6, 2025
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This introduces a new param which prevents Pyrodigal from appending
*to coding sequences which contain a stop codon. It has been reported in #373 that AMPlify ignores sequences containing non-sequence characters like*, thus this Pyrodigal flag should be used.The other annotation tools don't have such a flag unfortunately. We could think about adding a filtering step before AMPlify execution if the AMPlify authors don't solve this upstream (see issue bcgsc/AMPlify#17).
PR checklist
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).