subworkflows_bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Documentation for bam_to_trimmed_fastq_and_biscuit_alignments.cwl

This page is auto-generated. Do not edit.

Overview

bam to trimmed fastqs and biscuit alignments

Inputs

Name	Label	Description	Type	Secondary Files
bam			File
adapters			File
adapter_trim_end			string
adapter_min_overlap			int
max_uncalled			int
min_readlength			int
read_group_id			string
reference_index			string

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File

Steps

Name	CWL Run
bam_to_fastq	tools/bam_to_fastq.cwl
trim_fastq	tools/trim_fastq.cwl
biscuit_align	tools/biscuit_align.cwl
index_bam	tools/index_bam.cwl
biscuit_markdup	tools/biscuit_markdup.cwl