Multiqc

MultiQC aggregates results from bioinformatics analyses across many samples into a single report.

Info

ID: multiqc
Namespace: qc

It searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -main-script target/nextflow/qc/multiqc/main.nf \
  --help

Run command

Example of params.yaml
# Arguments
input: # please fill in - example: ["input.txt"]
# output: "$id.$key.output.output"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/qc/multiqc/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument group

Arguments

Name Description Attributes
--input Inputs for MultiQC. List of file, required, example: "input.txt", multiple_sep: ":"
--output Create report in the specified output directory. file, required, example: "report"