flowcraft.templates.skesa module

Purpose

This module is intended execute Skesa on paired-end FastQ files.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

  • sample_id : Sample Identification string.
    • e.g.: 'SampleA'
  • fastq_pair : Pair of FastQ file paths.
    • e.g.: 'SampleA_1.fastq.gz SampleA_2.fastq.gz'
  • clear : If ‘true’, remove the input fastq files at the end of the
    component run, IF THE FILES ARE IN THE WORK DIRECTORY

Generated output

  • ${sample_id}_*.assembly.fasta : Main output of skesawith the assembly
    • e.g.: sample_1_skesa.fasta
  • clear : If ‘true’, remove the input fastq files at the end of the
    component run, IF THE FILES ARE IN THE WORK DIRECTORY

Code documentation

flowcraft.templates.skesa.clean_up(fastq)[source]

Cleans the temporary fastq files. If they are symlinks, the link source is removed

Parameters:
fastq : list

List of fastq files.