Merge BAM Files Element

Merge BAM files using SAMTools merge.

Element type: merge-bam

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
Output directorySelect an output directory. Options include: Custom - specify the output directory in the ‘Custom directory’ parameter; Workflow - internal workflow directory; Input file - the directory of the input file.
out-modenumeric
Custom directoryCustom output directory.custom-dirstring
Output BAM nameA name for the output BAM file. If a default or empty value is provided, the output name is the name of the first BAM file with a .merged.bam extension.out-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
« Improve Reads with Trimmomatic Element Remove Duplicates in BAM Files Element »