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tweaks filtered fastq filenames and limits large file outputs #3

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tweaks filtered fastq filenames and limits large file outputs #3

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Two updates intended to improve routine implementation within PDL:

  1. adjust final filtered fastq filenames for smoother integration with existing downstream processes
  2. add new boolean parameter (keep_big_files) for user control over saving (or not) large intermediate files, particularly *.bam files and partially-filtered fastq files.

@mikeyweigand mikeyweigand self-assigned this Dec 10, 2024
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