Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop Illumina (FASTQ) data as well as to remove adapters.
Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Input data | Set the type of the input reads: single-end (SE) or paired-end (PE). | SE reads |
Trimming steps | Configure trimming steps that should be performed by Trimmomatic. | configure steps |
Output file | Specify the output file name. | auto |
Generate detailed log | Select "True" to generate a file with log of all read trimmings, indicating the following details (-trimlog):
| False |
Number of threads | Use multiple threads (-threads). | 8 |
To configure trimming steps use the following button:
Parameters in Workflow File
Type: trimmomatic
Parameter | Parameter in the GUI | Type |
---|---|---|
input-data | Input data | string |
trimming-steps | Trimming steps | string |
output-url | Output file | string |
generate-log | Generate detailed log | bool |
threads | Number of threads | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input FASTQ file(s)
Name in Workflow File: in
Slots:
Slot In GUI | Slot in Workflow File | Type |
---|---|---|
Input FASTQ URL | reads-url1 | string |
And 1 output port:
Name in GUI: Improved FASTQ file(s)
Name in Workflow File: out-file
Slots:
Slot InGUI | Slot in Workflow File | Type |
---|---|---|
Output FASTQ URL | reads-url1 | string |