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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
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declaration for "$maxn_fraction" #152

Closed manogenome closed 1 year ago

manogenome commented 1 year ago

Fixing a minor bug. Just added a declaration for "$maxn_fraction"


Global symbol "$maxn_fraction" requires explicit package name (did you forget to declare "my $maxn_fraction"?) at ./trim_galore line 657.
FelixKrueger commented 1 year ago

Dear Manoj,

thanks for acting on this so quickly. I had learned about the issue last night as the Bioconda build didn't pass the checks, so I was about to fix it this morning anyway.

The issue arose because of merging some commits that were made against the mater branch, and some from the dev branch, which resulted in merge conflicts - which I evidently didn't resolve in the correct way... So for future reference, PR should be filed against the dev branch.

I have now fixed the declaration of the max_n fraction (it had to go at a somewhat different place, see here), so I will close this PR. Thanks again, Felix

manogenome commented 1 year ago

Thanks, Felix. I was helping a friend set up the nextflow RNASeq pipeline on his laptop earlier when I noticed the issue. I'll send any future PR to the dev branch.