Snakemake Rule 2: Create spaceranger object

This step creates a spaceranger-style object for the newly transformed MSI data.

Input

• New MSI coordinates and image: output/[sample]/transformed.csv, output/[sample]/transformed.png

• MSI intensities: input/[sample]/msi/MSI_intensities.csv

Parameters

• verbose determines how much information about different stages of the process is delivered to the user

Output

• MSI in spaceranger style: output/[sample]/spaceranger/

Code (from Snakemake file)

rule make_spaceranger:
    message:
        "Creating spaceranger formatted output."
    conda: 'magpie'
    input:
        "output/{sample}/transformed.csv",
        "output/{sample}/transformed.png"
    output:
        "output/{sample}/spaceranger/filtered_feature_bc_matrix.h5"
    params:
        sample = "{sample}",
        verbose = True
    script:
        "scripts/create_mock_spaceranger.py"