add STAR in PG paired detection

[WardDeb]

Hi,

I've hit a case where I have single-end data aligned with STAR. Running with flags:

--snp_file SNPgenome/all_CAST_EiJ_SNPs_C57BL_6NJ_reference.based_on_GRCm38.txt
--no_sort
-o RNAsplit

gave me the error:

Unable to detect library type automatically, please specify whether the file is single- or paired-end manually

It doesn't seem that I can specify single-end (as --paired is a flag).
Adding the ID:STAR circumvents this error, though I'm not sure if it makes sense to solve this here (not really familiar with perl).

Kind regards,

WardDeb

[FelixKrueger]

Hi @WardDeb

Sorry hadn't realised you submitted a PR; I have now tried to implement an option --single_end that should allow you to skip the paired-end auto-detection altogether. Can you please clone the dev version and see if it now works for you?

[WardDeb]

Works as a charm,

thanks a lot !

[FelixKrueger]

Glad to hear it, thanks for bringing this to my attention!