pipelines

List of pipelines CWLs

This list is auto-generated. Do not edit.

CWL	Description
alignment_exome.cwl	exome alignment with qc
alignment_exome_nonhuman.cwl	exome alignment with qc, no bqsr, no verify_bam_id
alignment_umi_duplex.cwl	umi duplex alignment fastq workflow
alignment_umi_molecular.cwl	umi molecular alignment fastq workflow
alignment_wgs.cwl	wgs alignment with qc
alignment_wgs_nonhuman.cwl	alignment for nonhuman with qc
aml_trio_cle.cwl	Replace legacy AML Trio Assay
aml_trio_cle_gathered.cwl	gather AML trio outputs
bisulfite.cwl	Bisulfite alignment and QC
chipseq.cwl	Chipseq alignment with qc and creating homer tag directory
chipseq_alignment_nonhuman.cwl	Chipseq alignment for nonhuman with qc and creating homer tag directory
detect_variants.cwl	Detect Variants workflow
detect_variants_nonhuman.cwl	Detect Variants workflow
detect_variants_wgs.cwl	Detect Variants workflow for WGS pipeline
detect_variants_wgs_nonhuman.cwl	Detect Variants workflow for nonhuman WGS pipeline
downsample_and_recall.cwl	Downsample and HaplotypeCaller
gathered_downsample_and_recall.cwl	Gathered Downsample and HaplotypeCaller
germline_exome.cwl	exome alignment and germline variant detection
germline_exome_gvcf.cwl	exome alignment and germline variant detection
germline_exome_hla_typing.cwl	exome alignment and germline variant detection, with optitype for HLA typing
germline_wgs.cwl	wgs alignment and germline variant detection
germline_wgs_gvcf.cwl	wgs alignment and germline variant detection
immuno.cwl	Immunotherapy Workflow
rnaseq.cwl	RNA-Seq alignment and transcript/gene abundance workflow
rnaseq_star_fusion.cwl	STAR-RNA-Seq alignment and transcript/gene abundance workflow
rnaseq_star_fusion_with_xenosplit.cwl	STAR-RNA-Seq alignment and transcript/gene abundance workflow with Xenosplit
somatic_exome.cwl	somatic_exome: exome alignment and somatic variant detection
somatic_exome_cle.cwl	exome alignment and somatic variant detection for cle purpose
somatic_exome_cle_gathered.cwl	gathered exome alignment and somatic variant detection for cle purpose
somatic_exome_gathered.cwl	gathered exome alignment and somatic variant detection
somatic_exome_nonhuman.cwl	exome alignment and somatic variant detection
somatic_wgs.cwl	Whole genome alignment and somatic variant detection
somatic_wgs_nonhuman.cwl	wgs alignment and somatic variant detection
tumor_only_detect_variants.cwl	Tumor-Only Detect Variants workflow
tumor_only_exome.cwl	exome alignment and tumor-only variant detection
tumor_only_wgs.cwl	wgs alignment and tumor-only variant detection