Error with Bismark methylation extractor gwcov option

[FelixKrueger]

The gwcov option (#bismark_methXtract gwcov) tries to find scripts in your home directory and thus fails. Cheers, Felix

• Error! Can't find capture regions BED file - running without capture information.
• Error! Couldn't find find the coverage script: /home/phil/scripts/visualizations/bismark/bismark_coverage_curves.pl
• Error! Couldn't find find the windows script: /home/phil/scripts/visualizations/bismark/bismark_window_sizes.pl

[ewels]

Yup, this is actually the desired behaviour. Unless I bundle these scripts with cluster flow (which I don't want to do) or assume that they are in the PATH (which seems unlikely), users will have to edit this module to include the location of their scripts.

The right way to do this would be to read the paths from the config file of course, but I'm hoping that this chunk of module will soon be replaced if and when they are incorporated into bismark ;)

Also, they should only throw a warning and not fail. Let me know if this isn't the case, and cluster flow is actually falling over because of it.

[ewels]

TODO: Remove the word 'error' from the warning so that it isn't flagged in the e-mail report.

[ewels]

Fixed in 73fcb65