Workflow: Bisulfite alignment and QC

Fetched 2023-01-04 10:51:13 GMT
children parents
Workflow as SVG
  • Selected
  • Default Values
  • Nested Workflows
  • Tools
  • Inputs/Outputs

Inputs

ID Type Title Doc
sample_name String
QCannotation File
read_group_id String[]
reference_index String
reference_sizes File
trimming_adapters 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

instrument_data_bams File[]
trimming_max_uncalled Integer
trimming_min_readlength Integer
trimming_adapter_trim_end String
trimming_adapter_min_overlap Integer

Steps

ID Runs Label Doc
merge
../tools/merge_bams.cwl (CommandLineTool)
Sambamba: merge
pileup
../tools/biscuit_pileup.cwl (CommandLineTool)
Biscuit pileup
vcf2bed
../tools/bisulfite_vcf2bed.cwl (CommandLineTool)
convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script
index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
bisulfite_qc Bisulfite QC tools
bedgraph_to_bigwig
../tools/bedgraph_to_bigwig.cwl (CommandLineTool)
bedGraph to bigwig conversion
bam_to_trimmed_fastq_and_biscuit_alignments bam to trimmed fastqs and biscuit alignments

Outputs

ID Type Label Doc
vcf File
cpgs File[]
cram File
cpg_bigwig File[]
gathered_directory Directory
Permalink: https://w3id.org/cwl/view/git/06d2440d115b446c299b4ce96e8812d2f8df86ec/definitions/pipelines/bisulfite.cwl