Reference index file is not optional for Manta

[davidcotter]

The documentation states that the index for the reference is optional:
--fai FAI (Optional) The name of the corresponding index for the reference genome file.

For Manta at least, if I omit the index, this caused it to fail with the following error message:

Usage: configManta.py [options]
configManta.py: error: Can't find expected fasta index file: '/home/dnanexus/ref.fa.fai'
python: can't open file '/home/dnanexus/manta/runWorkflow.py': [Errno 2] No such file or directory

If I include the reference index Manta runs. Perhaps this could be a mandatory parameter or the index could be generated.

I am using the docker image dnanexus/parliament2

Thanks.

[slzarate]

Hi @davidcotter, let me look into this, as the FAI should be generated automatically if not included. Thanks for using Parliament2!

Also, can you use the Docker image dnanexus/parliament2:0.1.9? That's the latest version.