FastQC module

This module allow to run FastQC v0.11.2 on fastq or sam files to generate a quality control report in HTML.

  • Internal name: fastqc
  • Available: Both local and distributed mode

  • Input port:
    • input: reads in FASTQ format (format: reads_fastq) or alignments in SAM format (format: mapper_results_sam)

  • Output port:
    • output: report in HTML format (format: fastqc_report_html)

  • Optional parameters:
    • Parameter Type Description Default value
    input.format string Define the input format file, it can be fastq or sam. It is different of sam, fastq is used. fastq
    fastqc.kmer.size integer Define the length of Kmer to look for in the Kmer content module. The specified Kmer length must be between 2 and 10. 7
    fastqc.nogroup boolean Enable or disable the grouping of bases for reads >50bp. false
    fastqc.expgroup boolean Enable or disable the use exponential base groups in graph. false
    fastqc.casava boolean Use FASTQ from casava/Illumina. false
    fastqc.nofilter boolean If true, bad Illumina quality reads will not be filtered. This option is only available with fastqc.casava=true. true
  • Configuration example:
    • <!-- FastQC step -->
<step id="myfastqcstep" skip="false" discardoutput="false">
        <module>fastqc</module>
        <parameters>
                <parameter>
                        <name>input.format</name>
                        <value>fastq</value>
                </parameter>
                <parameter>
                        <name>fastqc.casava</name>
                        <value>true</value>
                </parameter>
        </parameters>
</step>