Reference genome "*.fasta" in addition to ".fa"

CGATOxford / CGATPipelines

Collection of CGAT NGS Pipelines

MIT License

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Reference genome "*.fasta" in addition to ".fa" #407

Closed kevinrue closed 6 years ago

kevinrue commented 6 years ago

https://github.com/CGATOxford/CGATPipelines/blob/48eba7d41297a268a622a4e5d98a5a5565af52be/CGATPipelines/PipelineMapping.py#L368

Could reference genomes be supported with both "fa" and "fasta" extensions? Or is there a particular reason/pipeline that should be used to ensure only "fa" are supported here?

Thanks!

Acribbs commented 6 years ago

I assume that this was because the UCSC convention is to name the fasta files of the reference genome .fa. @AndreasHeger can probably shed more light.

kevinrue commented 6 years ago

Nevermind, I need to learn how to read comments in pipeline.ini:

# location of indexed genome, needs to be set
genome_dir=/gfs/mirror/genomes/plain # <<<< should have been /gfs/mirror/genomes/index in my case

Sorry for the waste of time -_-