Workflow Documentation

from latch import workflow

@workflow
def rnaseq(
    ...
):
    """Perform alignment and quantification on Bulk RNA-Sequencing reads.

    ...
    """
    ...

from latch import workflow

@workflow
def rnaseq(
    ...
):
    """Perform alignment and quantification on Bulk RNA-Sequencing reads

    Bulk RNA-Seq (Alignment and Quantification)
    ----
    This workflow will produce gene and transcript counts from bulk RNA-seq
    sample reads.

    # Disclaimer

    This workflow assumes that your sequencing reads were derived from *short-read
    cDNA seqeuncing* ...

    # Brief Summary of RNA-seq

    This workflow ingests short-read sequencing files (in FastQ format) that came
    from the following sequence of steps[^1]:
      - RNA extraction from sample
      - cDNA synthesis from extracted RNA
      - adaptor ligation / library prep
      - (likely) PCR amplification of library
      - sequencing of library
    You will likely end up with one or more FastQ files from this process that hold
    the sequencing reads in raw text form. This will be the starting point of our
    workflow.
    ...
    """