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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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Allow the users to specify their own MTB references #53

Open abhi18av opened 2 years ago

abhi18av commented 2 years ago

A first attempt to the problem was made here https://github.com/mtb-bioinformatics/mtbseq-nf/issues/31

However, refererring the manual for MTBseq, it doesn't seem like an entire location could be passed

--ref This OPTION sets the reference genome for the read mapping. By default, the genome of Mycobacterium tuberculosis H37Rv (NC_000962.3) is set as reference. User supplied FASTA files for other reference genomes should be placed in the directory /MTBseq_source/var/ref/, and the respective name given without .fasta extension.

Therefore, for the time being, we'll only accomodate the annotations file.

Mxrcon commented 2 years ago

hmm, makes sense! this was the problem that i was having on the accommodation of reference files.