FastQC Quality Control Element

This element generates quality control reports for short read sequencing data using FastQC.

Element type: fastqc

Parameters

Parameter	Description	Default Value	Parameter in Workflow File	Type
Output file	Name of the resulting FastQC report file. If not set, the input file name is used.	Input file	`out-file`	string
List of adapters	Optional file with adapter sequences. Format: `name<TAB>sequence`. Lines starting with `#` are ignored.	(not set)	`adapter`	string
List of contaminants	Optional file with contaminants to screen for. Same format as adapters.	(not set)	`contaminants`	string

Input/Output Ports

Input Port

Name in GUI	Name in Workflow File	Slot	Slot in Workflow File	Type
`Short reads`	`in-file`	Source URL	`url`	string

Example

You can use this element to generate FastQC reports in a larger workflow:

ugene workflow run \
  --element fastqc \
  --url input_reads.fastq \
  --out-file fastqc_report.html

If you wish to customize adapter or contaminant lists:

ugene workflow run \
  --element fastqc \
  --url input.fastq \
  --adapter my_adapters.txt \
  --contaminants my_contaminants.txt \
  --out-file output_report.html

Adapter and contaminant files must contain tab-separated name<tab>sequence entries. Lines starting with # are ignored.