https://github.com/dfornika/callvariants-with-codons
https://github.com/dfornika/callvariants-with-codons
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/dfornika/callvariants-with-codons
- Owner: dfornika
- Created: 2020-12-24T20:02:33.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2020-12-24T20:04:19.000Z (over 4 years ago)
- Last Synced: 2025-01-24T23:49:08.671Z (4 months ago)
- Language: Nextflow
- Size: 1.95 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# callVariantsWithCodons
This is a small supplementary workflow that takes an existing output directory from [BCCDC-PHL/ncov2019-artic-nf](https://github.com/BCCDC-PHL/ncov2019-artic-nf)
and re-runs the `callVariants` process (using `ivar variants`), with a `.gff` annotation file. This produces an output `variants.tsv` file with codon and
amino-acid information included. That information is missing from our default pipeline because we do not supply a `.gff` annotation file.
The pipeline is intended to be used to add new output files into an existing pipeline output directory. To prevent overwriting the existing `variants.tsv` files,
the output from this pipeline is written to a separate output directory and the output filenames have been appended with `.aa.tsv`.
After running this pipeline, the output directory would have two `variants.tsv` output directories, as follows:
```
ncovIllumina_sequenceAnalysis_callVariants/.variants.tsv
ncovIllumina_sequenceAnalysis_callVariantsWithCodons/.variants.aa.tsv
```
## Usage
```
nextflow run dfornika/callVariants-with-codons \
-profile conda \
--artic_analysis_dir \
--ref \
--gff \
--outdir
```