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Builds quality control reports.

Parameters in GUI

ParameterDescriptionDefault value
Output directorySelect an output directory. Custom - specify the output directory in the 'Custom directory' parameter. Workflow - internal workflow directory. Input file - the directory of the input file.Input file
List of adapters

Specifies a non-default file which contains the list of adapter sequences which will be explicity searched against the library. The file must contain sets of named adapters in the form name[tab]sequence. Lines prefixed with a hash will be ignored.

 
List of contaminantsSpecifies a non-default file which contains the list of contaminants to screen overrepresented sequences against. The file must contain sets of named contaminants in the form name[tab]sequence. Lines prefixed with a hash will be ignored. 

Parameters in Workflow File 

Type: fastqc

ParameterParameter in the GUIType
out-modeOutput directorystring
adapterList of adaptersstring
contaminantsList of contaminantsstring

Input/Output Ports

The element has 1 input port:

Name in GUI: Short reads

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring
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