skesa

Purpose

This components assembles paired-end FastQ files using the Skesa assembler.

Input/Output type

  • Input type: FastQ
  • Output type: Fasta

Note

The default input parameter for FastQ data is --fastq. You can change the --fastq parameter default pattern (fastq/*_{1,2}.*) according to input file names (e.g.: --fastq "path/to/fastq/*R{1,2}.*").

Parameters

None.

Published results

  • results/assembly/skesa: Stores the fasta assemblies for each sample.

Published reports

None.

Default directives

  • cpus: 4
  • memory: 5GB (dynamically increased on retry)
  • container: flowcraft/skesa
  • version: 2.3.0-1
  • scratch: true

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