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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
472 stars 151 forks source link

FastQC location as argument to trim_galore #122

Closed niekwit closed 3 years ago

niekwit commented 3 years ago

Is it possible to parse the FastQC directory to trim_galore if it is not set in $PATH? Thank you.

FelixKrueger commented 3 years ago

I think you can't pass it as an argument, but you can just modify this line in trim_galore to paste in the full path to the FastQC executable:

https://github.com/FelixKrueger/TrimGalore/blob/eb0480424b36fb22027e351869c669b8dc77335b/trim_galore#L456

niekwit commented 3 years ago

Thank you, that will help me out.