Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: master
workflow graph Filter single sample sv vcf from depth callers(cnvkit/cnvnator)

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/sv_depth_caller_filter.cwl

Branch/Commit ID: downsample_and_recall
workflow graph gaps_or_not.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: gaps_or_not.cwl

Branch/Commit ID: master
workflow graph QIIME2 Step 2 (DADA2 option)

QIIME2 DADA2, feature summaries, phylogenetic diversity tree, taxonomic analysis and ancom

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

Path: packed/qiime2-step2-dada2.cwl

Branch/Commit ID: qiime2-workflow

Packed ID: main
workflow graph ST520101.cwl

https://github.com/Marco-Salvi/cwl-ro-crate.git

Path: ST520101.cwl

Branch/Commit ID: main
workflow graph fastq_contamination_cleanup

This workflow detect and remove contamination from a DNA fasta file

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

Path: workflows/Contamination/fastq-contamination-cleanup.cwl

Branch/Commit ID: master
workflow graph hi-c-processing-bam.cwl

https://github.com/4dn-dcic/docker-4dn-hic.git

Path: cwl/hi-c-processing-bam.cwl

Branch/Commit ID: master
workflow graph wf_full_IDR_pipeline_1input_sample.cwl

This workflow essentially restructures the inputs before sending to wf_full_IDR_pipeline_1input.cwl

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

Path: cwl/wf_full_IDR_pipeline_1input_sample.cwl

Branch/Commit ID: master
workflow graph wf-alignment.cwl

https://github.com/farahzkhan/bcbio_test_cwlprov.git

Path: somatic/somatic-workflow/wf-alignment.cwl

Branch/Commit ID: master
workflow graph Calibration inputs to Simulation Model

This workflow produces calibration inputs to simulation model: - atmospheric model - extinction hypercube - telescopes' cameras configurations - telescopes' PSFs - optical throughput

https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git

Path: workflows/calibpipe/uc-cp-001.cwl

Branch/Commit ID: main