Remove intermediate files after processing

NAL-i5K / NAL_RNA_seq_annotation_pipeline

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Remove intermediate files after processing #38

Closed mpoelchau closed 4 years ago

mpoelchau commented 4 years ago

The RNAseq_annotate.py program downloads a lot of large files, which are not needed after the program has finished (except for debugging purposes).

Everything should be deleted, except for the final output files; the log files (basically anything ending in .log or .errlog, including in the SRR subdirectories); and source.txt.

It would also be nice if there were a 'debug' argument that would turn the delete behavior off (so, deleting the files would be the default).

HsiuKangHuang commented 4 years ago

Okay! I will also remove .hs2 files and normalized fastq files after the process. Users can remove option "-t" in sbatch.sh file if they don't want to keep them.

mpoelchau commented 4 years ago

Tested, works!