Add '.fq' and '.fq.gz' to accepted file extensions

[mckellardw]

I am trying to add miRge3 to one of my pipelines, and hit a snag where it does not accept '.fq.gz' files- WARNING: File file.fq.gz is neither fastq or fastq.gz format!. Could you add these extensions to the accepted options?

[mckellardw]

One more request- is there a way to remove the extra date/numbers that is appended onto the output directory name? They make it difficult to work with in workflow managers like snakemake where the file names need to be predictable. Thanks!

[arunhpatil]

Hi @mckellardw,

Thanks for your inputs. Regarding the output directory name, It (by default) has a suffix of date and time. This would be ideal to avoid names with space or special characters. However, you could pass this hidden argument '-onam' or '--outDirName' with the name of the directory and this should solve the problem. Please let me know if you have any further questions.

I have added the change to include fq.gz extension at miRge3.0.miRgeEssential , but this won't reflect until I make the new release. However, will already be part in the next release.

Thank you for your suggestions.
Arun

[mckellardw]

Thanks very much!