Explore Workflows

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-2.cwl

Branch/Commit ID: dev

https://gitlab.com/ellip-ogc-eo-apps/cwl.git

Path: fan-out/stage-in/wrapper.cwl

Branch/Commit ID: master

Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. These inputs are all required to be sorted in the same order: sample_ids patient_ids sample_classes unfiltered_pileups duplex_pileups

https://github.com/mskcc/access-pipeline.git

Path: workflows/subworkflows/find_hotspots_in_normals.cwl

Branch/Commit ID: master

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/icgc-tcga-pancancer/pcawg-snv-indel-annotation.git

Path: preprocess_vcf.cwl

Branch/Commit ID: master

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 0cd2d70

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: master

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/cache_test_workflow.cwl

Branch/Commit ID: main

https://github.com/cr-ste-justine/chujs-alignment-workflow.git

Path: workflows/wgsp_alignment_fq_wf.cwl

Branch/Commit ID: dev

Differential abundance testing with ANCOM from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

https://github.com/Duke-GCB/bespin-cwl.git

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: qiime2-workflow-paired

Packed ID: qiime2-09-ancom.cwl

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

Path: tests/count-lines8-wf-noET.cwl

Branch/Commit ID: main