This component performs a mapping procedure of FastQ files with a given reference. The procedure is carried out with Bowtie2. The reference can a set of Bowtie2 index files or a Fasta file. In the latter, the necessary index will be created with Bowtie2-build and passed through to Bowtie2.


Input/Output type

  • Input type: FastQ
  • Output type: Bam


The default input parameter for Fastq data is --fastq.


  • reference: Specifies the reference genome to be provided to to bowtie2-build.
  • index: Specifies the reference indexes to be provided to bowtie2.


An index OR a reference fasta file must be provided

Published results

  • results/mapping/bowtie: Stores the results of the mapping for each sample.

Published reports


Default directives

  • bowtie_build:
    • cpus: 1
    • memory: 5GB (dynamically increased on retry)
    • container: flowcraft/bowtie2_samtools
    • version: 1.0.0-1
  • bowtie:
    • cpus: 4
    • memory: 5GB (dynamically increased on retry)
    • container:flowcraft/bowtie2_samtools
    • version: 1.0.0-1