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pipelines

APipe Tester edited this page Dec 20, 2021 · 7 revisions

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
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