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Add functionality for SINGLE END samples #78

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slsevilla opened this issue Jun 8, 2023 · 0 comments
Open
8 tasks

Add functionality for SINGLE END samples #78

slsevilla opened this issue Jun 8, 2023 · 0 comments
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enhancement New feature or request

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@slsevilla
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Describe what enhancement you'd like to see.
Yue has requested that the pipeline have the capability to handle both paired end and single end sequencing data. To accomplish this, the following updates would need to be made

  • add a single/paired flag to the snakemake.config file
  • update the init.smk to process single/paired end reads differently
  • update align.smk
    • trim
    • align
  • update qc.smk
    • qc_fastqc
    • multiqc
@slsevilla slsevilla added the enhancement New feature or request label Jun 8, 2023
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@slsevilla