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urmi-21 / pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
MIT License
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cannot change the output dir for stringtie merge #3

Closed lijing28101 closed 4 years ago

lijing28101 commented 4 years ago

After running stringtie for each sample, I want to merge the gtf by stringtie merge. But the output was written to a SRR folder, not the working folder, and the name has SRR1573523_hisat2_sorted_stringtie prefix, which cannot change

st.stringtie_merge(*tuple(gtfList),out_suffix="maizeMerged",**{"-p":"16"})
urmi-21 commented 4 years ago

I have now added the parameter out_dir to the stringtie_merge function. If no out_dir is specified, merged file will be written in the same directory as the first input file. 51e27aaafce2c0833b9142636c112587e87f98a8