MultiQC module
This module allow to run MultiQC on Eoulsan step output to generate a quality control report in HTML.
- Internal name: multiqc
- Available: Both local and distributed mode
- Input port:
- input1: FastQC report (format: fastqc_report_zip) if fastqc report is enabled
- input2: Mapper log (format: mapper_results_log) if mapreads report is enabled
- input3: Expression output (format: expression_results_tsv) if expression report is enabled
- Output port:
- output: report in HTML format (format: multiqc_report_html)
- Optional parameters:
| Parameter |
Type |
Description |
Default value |
| reports |
string |
Define the reports to generate. The available reports are listed in the following table. Several reports can be generated by separating their names with comma |
fastqc |
| use.docker |
boolean |
Enable Docker usage to execute MultiQC |
false |
| docker.image |
string |
The docker image to use when Docker is enabled |
ewels/multiqc:v1.7 |
- This module currently support the following reports:
| Eoulsan report name |
MultiQC section name |
Note |
| fastqc |
FastQC |
|
| mapreads |
The MultiQC section name change against the mapper used in the workflow (e.g. Bowtie 1/Bowtie 2/STAR...) |
Warning: this report is not available in Hadoop mode. |
| expression |
HTSeq Count |
|
| featurecounts |
FeaturesCounts |
|
- Configuration example:
<!-- MultiQC step -->
<step id="mymultiqcstep" skip="false" discardoutput="false">
<module>multiqc</module>
<parameters>
<parameter>
<name>reports</name>
<value>fastqc,mapreads,expression</value>
</parameter>
<parameter>
<name>use.docker</name>
<value>false</value>
</parameter>
</parameters>
</step>
