Fastqc

Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.

Info

ID: fastqc
Namespace: qc

Links

Source

This component can take one or more files (by means of shell globbing) or a complete directory

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 1.0.1 -latest \
  -main-script target/nextflow/qc/fastqc/main.nf \
  --help

Run command

Example of params.yaml

# Arguments
mode: "files"
input: # please fill in - example: "fastq_dir/"
# output: "$id.$key.output.output"
# threads: 123

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/qc/fastqc/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
--mode	The mode in which the component works. Can be either files or dir.	string, default: "files"
--input	Directory containing input fastq files.	file, required, example: "fastq_dir"
--output	Output directory to write reports to.	file, required, example: "qc"
--threads	Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory.	integer