retrieve_mapped

Purpose

This component retrieves the mapping reads of a previous bowtie mapping process. The procedure is carried out with samtools and aims to retrieve the reads that map to target reference.

Note

  • samtools documentation can be found here.

Input/Output type

  • Input type: bam
  • Output type: FastQ

Note

This process has the bowtie2 process as a dependency.

Parameters

None

Published results

  • results/mapping/retrieve_mapped: Contains the resulting FastQ files.

Published reports

None.

Default directives

  • remove_host:
    • cpus: 2
    • memory: 5GB (dynamically increased on retry)
    • container: flowcraft/bowtie2_samtools
    • version: 1.0.0-1