pipelines_bisulfite.cwl

Documentation for bisulfite.cwl

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Overview

Bisulfite alignment and QC

Inputs

Name	Label	Description	Type	Secondary Files
reference_index			string
reference_sizes			File
instrument_data_bams			File[]
read_group_id			string[]
sample_name			string
trimming_adapters			File
trimming_adapter_trim_end			string
trimming_adapter_min_overlap			int
trimming_max_uncalled			int
trimming_min_readlength			int
QCannotation			File
assay_non_cpg_sites		Variable to determine if user wants to obtain obtain bed/bigwig files for non-CpG cytosines. Value - true or false	{'type': 'enum', 'symbols': ['true', 'false']}

Outputs

Name	Label	Description	Type	Secondary Files
cram			File	['.crai', '^.crai']
vcf			File
cpgs			File[]
cpg_bigwig			File[]
gathered_directory			Directory

Steps

Name	CWL Run
bam_to_trimmed_fastq_and_biscuit_alignments	subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl
merge	tools/merge_bams.cwl
pileup	tools/biscuit_pileup.cwl
bisulfite_qc	subworkflows/bisulfite_qc.cwl
vcf2bed	tools/bisulfite_vcf2bed.cwl
bedgraph_to_bigwig	tools/bedgraph_to_bigwig.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl