qc/fastqc

Description

Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.

Type

bash_script

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
mode: [ "files" ]  
output: "$id.$key.output.qc"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/qc/fastqc/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--mode -m	string	The mode in which the component works. Can be either files or dir.
--input -i	file required	Directory containing input fastq files.
--output -o	file required output	Output directory to write reports to.
--threads -t	integer	Specifies the number of files which can be processed simultaneously. Each thread will be allocated 250MB of memory.

Name

Type & Properties

--mode

-m

string

--input

-i

file

required

--output

-o

file

required

output

--threads

-t

integer