Comments (3)
We've hit a problem with optionally including annotated contigs as input.
I've actually got this working, however the code has got quite messy now. But this has also led to two issues which makes me feel like I would rather not support this:
- DeepARG takes as input specifically nucleotide fasta out of PROKKA. Therefore if we don't run PROKKA on those samples that are supplied with the annotation fasta file, then those samples will not be executed by PROKKA. I.e. we would always have to run PROKKA on everything anyway regardless
- After thinking about it, I am also now concerned about version and software consistency. By allowing users supply their own FAA files, this could be from versions different from what we have in the pipeline, and in fact could be from different tools that may not be supported by other steps of our pipeline.
Therefore I would actually rather not support this. If you're concerned about speed, you could just Prodigal instead.
What do you think about this?
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Where I got to: 8bf973f
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I got an OK to skip this from Martin, and with the addition of Prodigal this should massively speed up the process anyway of those who are concerned about run time.
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Related Issues (20)
- Remove warning about broken DeepBGC database links from docs HOT 1
- Add missing essential parameters for antismash HOT 4
- Fix BAKTA publish dir HOT 1
- Split input assemblies into BGC vs ARG/AMP compatible length types HOT 1
- Workflow diagram is broken in `dev` HOT 1
- GUNZIP module is confused by repeated patterns in sample name and fasta path. HOT 2
- deeparg 1.0.4 required to correctly fetch DBs HOT 1
- AMPLIFY_PREDICT exits with a ValueError while checking input HOT 1
- In some cases RGI will not produce all files expected for mving for publishing HOT 5
- The spliting of contigs into _long and _short should only be performed when needed, or at least it should be skippable HOT 1
- Missing abricate database download instructions in usage
- Missing icons for BGC sections in nextflow schema/parameter docs
- improving tool documentation & adding tests HOT 1
- A uniform input for all tools in each screening workflow HOT 2
- Missing Annotation files HOT 2
- Antismash parameter bug HOT 1
- Consider allowing annotation to run even if downstream screening not run
- A special samplesheet can delete all my sequences HOT 3
- nf-test wishlist
- comBGC column BGC_length inaccurate HOT 3
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