cropping

This module handles everything about the cropping of the reads.

cropping.detectFilesToCrop(sras)

It reads the FastQC results for each run and decides whether they should be cropped or not depending on the quality of the reads.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

Returns:

list: List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

cropping.runTrimGalore(sras)

Crops the given runs using Trim Galore.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID

cropping.runTrimmomatic(sras)

Crops the given runs using Trimmomatic.

Args:

sras (list): List of tuples with the following data:

• A list of the paths for the input run (one file if single-end, two if paired-end)

• Run type. “single” if single-end, “paired” if paired-end

• Run ID