Remove PCR duplicates of BAM files using SAMTools rmdup.
Element type: rmdup-bam
Parameters
| Parameter | Description | Default value | Parameter in Workflow File | Type |
|---|---|---|---|---|
| Output directory | Select 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 | out-mode | numeric |
| Output BAM name | A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention. | out-name | string | |
| Remove for single-end reads | Remove duplicate for single-end reads. By default, the command works for paired-end reads only (-s). | False | remove-single-end | boolean |
| Treat as single-end | Treat paired-end reads and single-end reads (-S). | False | treat_reads | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: Input File
Name in Workflow File: in-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |
And 1 output port:
Name in GUI: Output File
Name in Workflow File: out-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |