In the default config.yaml on github, there is an example option like so:
config.yaml, line 37: star: "--outSAMtype BAM Unsorted"
However, if left in the config file it causes an error because then the STAR step gets two "--outSAMtype" flags. I realise defaults are meant to be changed, but I don't think this particular example can ever be used (because the flag is already hard-coded into the workflow).
dlaehnemann
commented
1 year ago
Good afternoon, thanks for the workflow!
In the default config.yaml on github, there is an example option like so:
config.yaml, line 37: star: "--outSAMtype BAM Unsorted"
However, if left in the config file it causes an error because then the STAR step gets two "--outSAMtype" flags. I realise defaults are meant to be changed, but I don't think this particular example can ever be used (because the flag is already hard-coded into the workflow).
Thanks again!
Matt.