mhalushka / miRge3.0

Comprehensive analysis of small RNA sequencing data
MIT License
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Add '.fq' and '.fq.gz' to accepted file extensions #66

Closed mckellardw closed 1 year ago

mckellardw commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Thanks very much!