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new option to keep simulated fastq files #6

@GrantHov

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@GrantHov

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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