Sort BAM Files Element
Sort BAM Files using SAMTools Sort.
Element type: Sort-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 | out-mode | numeric | |
| Custom directory | Specify the output directory. | custom-dir | string | |
| Output BAM name | A name for the output file. If the default or an empty value is provided, the output name is the name of the first file with an additional extension. | out-name | string | |
| Build index | Build index for the sorted file with SAMTools index. | human.hg18 | index | boolean |
Input/Output Ports
The element has 1 input port:
Name in GUI: BAM 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: Sorted BAM File
Name in Workflow File: out-file
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Source URL | url | string |