Cleanup temp alignment BAM files before usage #1
Description
Hello,
a test run on a fresh code of your pipeline with all the dependencies installed in cwd did not work. More specifically, it failed with the following errors: needLargeMem: trying to allocate 0 bytes (limit: 10000000000) this occurs when bedGraphToBigWig tries to work on an empty file as an input.
After a lot of digging in your code, I found the reason in line 828: find ${TMPDIR} -name "*.sort.bam" -size -1024k -delete this line deleted the *.sort.bam temp files before bedtools bamtobed had a chance to convert them. Thus the bedtools commands failed with a suppressed error (kill.warnings) and the std_out created empty bed.gz files which were given as input to bedGraphToBigWig.
The simple fix I implemented is just commenting out line 828, but I wanted to post it here in case a better fix can be implemented.