tools_hisat2_align.cwl

Documentation for hisat2_align.cwl

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Overview

HISAT2: align

Docker Requirement

mgibio/hisat2-sambamba:0.1

Inputs

Name	Label	Description	Type	Secondary Files
reference_index			File	['.1.ht2', '.2.ht2', '.3.ht2', '.4.ht2', '.5.ht2', '.6.ht2', '.7.ht2', '.8.ht2']
fastq1			File
fastq2			File
read_group_id			string
read_group_fields			{'type': 'array', 'items': 'string', 'inputBinding': {'prefix': '--rg'}}
strand			['null', {'type': 'enum', 'symbols': ['first', 'second', 'unstranded']}]

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File