cropping

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

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