Pipeline exits when there are no non-synonymous mutations

[johnoooh]

Description of the bug

When a maf is input that does not contain any non-synonymous mutations the generatemutfasta module will generate an empty fasta. This then causes an error in netmhcpan which will exit the pipeline.

A few option here to fix this:

• Detect if there are non-synonymous mutations in the Maf in input validation and end there for this sample. I dont like this solution as what if there is a sv bedpe that does have non-syn mutations as well. Would need to check both which may be difficult.
• If no nonsynonymous mutations are detected in the generatemutfasta page we output one synonymous mutation to the fastas. This will be filtered out later as the pipeline will detect that the Mut_sequence==WT_sequence.
• In Netmhcpan if the fasta is empty, dont run netmhcpan, just touch the requisite outputs so it moves along fine. This might cause errors later on in other modules.

Also, what is the best way to inform people that they don't have any non-syn mutation in their MAF?

This was discovered in Martina's pipeline run

Command used and terminal output

No response

Relevant files

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System information

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