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TBD!!!
Currently, the default behaviour of the crossmapper is to simulate fastq files for different species, concatenate them into one fastq file, and keep it in wgsim_ouput directory.
This default behaviour should be changed to removing fastq files after successful crossmapper run. We can implement a new option called --keep-fq which will enable the current behavior, which by default will be off.
We can add this new argument to crossmapper.py
:
shardParser.add_argument("--keep_fq", "--keep_fq", action = "store_true", default = False,
help = "Keep simulated fastq files. If specified, the simulated fastq files (which are not gz-ipped) will be kept. By default, fastq files are removed after the successful crossmapepr run to save space")
We can write a corresponding function in the helpers.py and execute it in crossmapper.py in the end
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