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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
467 stars 151 forks source link

cutadapt cores option docs are misleading #123

Closed keiranmraine closed 3 years ago

keiranmraine commented 3 years ago

Hi,

The cli docs indicate:

-j/--cores INT Number of cores to be used for trimming [default: 1]. For Cutadapt to work with multiple cores, it requires Python 3 as well as parallel gzip (pigz) installed on the system. The version of Python used is detected from the shebang line of the Cutadapt executable (either 'cutadapt', or a specified path). If Python 2 is detected, --cores is set to 1.

This doesn't appear to match the code as that specifically looks at the version of the actual tool, not python itself:

https://github.com/FelixKrueger/TrimGalore/blob/eb0480424b36fb22027e351869c669b8dc77335b/trim_galore#L783-L819

It looks like the reading of the #! was stopped ~3 years ago.

FelixKrueger commented 3 years ago

Thanks for spotting this, I have now changed the text for --help and in the User Guide to reflect this (at least to some extent), (811f364261e48898672505a9a5ee439353532c07).