Pyrodigal #251
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Pyrodigal #251
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louperelo
approved these changes
Mar 29, 2023
docs/usage.md
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| @@ -82,7 +82,7 @@ To prevent entire pipeline failures due to a single 'bad sample', nf-core/funcsc | |||
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| When the annotation is run with Prokka, the resulting `.gbk` file passed to antiSMASH may produce the error `translation longer than location allows` and end the pipeline run. This Prokka bug has been reported before (see [discussion on GitHub](https://github.com/antismash/antismash/discussions/450)) and is not likely to be fixed soon. | |||
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| > ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead leave the default annotation tool Prodigal or switch to Bakta (for bacteria only!). | |||
| > ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead leave the default annotation tool Pyrodigal or switch to Bakta (for bacteria only!). | |||
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Did you set Pyrodigal as default now? I think the nextflow.config hasn't been changed, right?
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| > ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead leave the default annotation tool Pyrodigal or switch to Bakta (for bacteria only!). | |
| > ⚠️ If antiSMASH is run for BGC detection, we recommend to **not** run Prokka for annotation but instead leave the default annotation tool Prodigal or switch to Bakta (for bacteria only!). If no gbk file is needed, Pyrodigal should be chosen as a faster alternative to Prodigal. It produces exactly the same results as Prodigal with lower memory usage. |
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Actually I would not go into details about Pyrodigal/Prodigal differences here, because this paragraph is about not using Prokka for Antismash. More detailed info about the annotation tool differences can be found at the parameters and output docs already.
jfy133
requested changes
Mar 29, 2023
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Apparently some little layout things were changed in all modules to make them appear nicer on the website (@mashehu said). |
jfy133
reviewed
Mar 29, 2023
jfy133
approved these changes
Mar 29, 2023
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Closes #213
PR checklist
nf-core lint).nextflow run . -profile 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).