Fasta File suffixes

[drtconway]

Hi Janis,

I'm getting the following warning:

2020-11-12T15:19:18 [WARN]: The input for 'fasta' (FastaFai) did not have the expected extension .fasta OR .fa: /data/reference/dawson_labs/genomes/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna.

An extension of .fna is pretty wide-spread for FASTA files, and is in some sense even preferable to .fa or .fasta since it specifically suggests it contains nucleotides (i.e. DNA or RNA) rather than, for example .faa which is used to contain amino acids, also in the FASTA format.

It'd be polite of Janis not to produce a warning in this case.

Thanks Tom.

[illusional]

Hi Tom, you're starting to see the start of Janis 0.11.x! There are a heap of really cool changes that are coming soon (and you're hitting a pre-release while accessing janis/dev. Some noteworthy things coming up:

• More checks on starting runs (to check your input data is in an expected / correct-ish format).
• Janis prepare:
  • This also includes checking contigs between Fasta references and Bed Files.
  • Moulding your almost-ready data into what we're expecting (eg: automatic converting VCFs into Compressed VCFs, automatic indexing of references depending on the pipeline).
• Evaluation of submissions to janis-bioinf (to check for correctness)
• Sweet testing suite to test the running of tools.

I've added a commit to janis-bioinf to add an alternate extension for Fasta, and I'll deploy this to the cluster soon.

[drtconway]

Cheers!