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  • Merge BAM Files Element
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Merge BAM files using SAMTools merge.

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. 
Custom directoryCustom output directory. 
Output BAM nameA name of an output BAM file. If default of empty value is provided the output name is the name of the first BAM file with .merged.bam extention. 

Parameters in Workflow File

Type: merge-bam

ParameterParameter in the GUIType
out-modeOutput directorynumeric
custom-dirCustom directory


out-nameOutput namestring

Input/Output Ports

The element has 1 input port:

Name in GUI: BAM File

Name in Workflow File: in-file


Slot In GUISlot in Workflow FileType
Source URLinput-urlstring

And 1 output port:

Name in GUI: Merged BAM files

Name in Workflow File: out-file


Slot In GUISlot in Workflow FileType
Source URLoutput-urlstring
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