subworkflows_sequence_to_trimmed_fastq_and_hisat_alignments.cwl

Documentation for sequence_to_trimmed_fastq_and_hisat_alignments.cwl

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Overview

sequence (bam or fastqs) to trimmed fastqs and HISAT alignments

Inputs

Name	Label	Description	Type	Secondary Files
unaligned			../types/sequence_data.yml#sequence_data
adapters			File
adapter_trim_end			string
adapter_min_overlap			int
max_uncalled			int
min_readlength			int
read_group_id			string
read_group_fields			{'type': 'array', 'items': 'string'}
reference_index			File	['.1.ht2', '.2.ht2', '.3.ht2', '.4.ht2', '.5.ht2', '.6.ht2', '.7.ht2', '.8.ht2']
strand			['null', {'type': 'enum', 'symbols': ['first', 'second', 'unstranded']}]
unzip_fastqs			boolean?

Outputs

Name	Label	Description	Type	Secondary Files
fastqs			File[]
aligned_bam			File

Steps

Name	CWL Run
sequence_to_fastq	tools/sequence_to_fastq.cwl
trim_fastq	tools/trim_fastq.cwl
hisat2_align	tools/hisat2_align.cwl