add TSV to VCF script to iVar Titan container #245
Merged
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This PR replaces #224 (see for previous discussion) so as to only affect the ivar-titan container, not the main one.
The PR adds a script, ivar_variants_to_vcf.py, to convert the iVar variants in TSV format to VCF. The script is pulled from nf-core/viralrecon v2.1 release.
ivar_variants_to_vcf.py
had/user/bin/env python
in it's shebang line, the container haspython3
in the path but notpython
. Rather than editingivar_variants_to_vcf.py
, I usedupdate-alternatives
to addpython
(just a symlink topython3
).Please let me know if there are any questions, or anything needed on my end.
Example Usage
Attaching inputs/outputs (w/ .txt extension to make GitHub happy)
20154160_S5_L001.variants.vcf.txt
20154160_S5_L001.variants.tsv.txt