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
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:We can write a corresponding function in the helpers.py and execute it in crossmapper.py in the end