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Remove PCR duplicates of BAM files using SAMTools rmdup.

Element type: rmdup-bam

Parameters

ParameterDescriptionDefault valueParameter in Workflow FileType
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.Input fileout-modenumeric
Output BAM nameA 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-namestring
Remove for single-end readsRemove duplicate for single-end reads. By default, the command works for paired-end reads only (-s).Falseremove-single-endboolean
Treat as single-end

Treat paired-end reads and single-end reads (-S).

Falsetreat_readsboolean

Input/Output Ports

The element has 1 input port:

Name in GUI: Input File

Name in Workflow File: in-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring

And 1 output port:

Name in GUI: Output File

Name in Workflow File: out-file

Slots:

Slot In GUISlot in Workflow FileType
Source URLurlstring
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