variations in mitochondrial chromosome name and its absence

current issue

Our pipeline fails when there is no mitochondrial chromosome in the samples that were basecalled and passed quality control, as mentioned in !19 by @nicolasecendron. This error occurs in step 3when conducting the modkit extract full command. However, either command that passes the option --region will result in this error if the chromosome is absent.

Error! contig-missing, MT

This error also occurs when the chromosome is labeled differently. Currently, there are three possibilities: chrM, chrMT or MT.

solution

1 - Choose between the three names: Implement a check for the mitochondrial chromosome name and automate the process of choosing a name.

2 - User notification: If chrM is absent, we should notify the user and guide them in resolving the issue.