Explore Workflows

The workflow is used to run CHIP-Seq basic analysis with single-end input FASTQ file. In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, reads coverage in a form of bigWig file, peaks calling data in a form of narrowPeak or broadPeak files.

https://github.com/Barski-lab/ga4gh_challenge.git

Path: biowardrobe_chipseq_se.cwl

Branch/Commit ID: v0.0.3

This workflow returns the reproducible number of split peaks given a single bam file and its size-matched input pair. This workflow splits the bam file first, but does not do anything to the input.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_split_self_and_idr.cwl

Branch/Commit ID: master

GATK4.2.4.1 Mutect2 workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: master

This is a subworkflow of the main oxog_varbam_annotat_wf workflow - this is not meant to be run as a stand-alone workflow!

https://github.com/ICGC-TCGA-PanCancer/OxoG-Dockstore-Tools.git

Path: oxog_sub_wf.cwl

Branch/Commit ID: 1.0.0

https://github.com/ICGC-TCGA-PanCancer/Seqware-BWA-Workflow.git

Path: checker-workflow-wrapping-workflow.cwl

Branch/Commit ID: 2.6.8_1.4

This workflow aligns the fastq files using magicblast for paired-end samples

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Alignments/magicblast-alignment.cwl

Branch/Commit ID: master

https://github.com/mr-c/4dn-dcic-pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-parta-juicer.cwl

Branch/Commit ID: dev2

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-007_nojs.cwl

Branch/Commit ID: main

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/upload_results.cwl

Branch/Commit ID: master

https://github.com/alpha-unito/streamflow-fl.git

Path: cwl/main.cwl

Branch/Commit ID: master