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location of output files #23

Closed giardine closed 3 years ago

giardine commented 3 years ago

I am continuing to get errors. It would be helpful if it didn't write to /tmp because then I could see the output that is generated and better determine the error. The current one appears to be a problem with STAR, but the error I get just says a missing final log file. Is there a parameter I can set to tell it where to write intermediate files?

byee4 commented 3 years ago

I believe cwltool can accept certain parameters to avoid having to write to tmp, for example our runner script uses --cachedir and --outdir to specify where the pipeline intermediates and outputs go, respectively.

giardine commented 3 years ago

Thanks, that helped a lot. The STAR error was likely problems with writing to /tmp as it now goes farther. It can't find makebigwigfiles. With previous errors it turned out the actual program has a different name, so I am off to search for it.