Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-valuefrom-wf5.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-valuefrom-wf5.cwl

Branch/Commit ID: master
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: downsample_and_recall
workflow graph EMG pipeline v3.0 (paired end version)

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

Path: workflows/emg-pipeline-v3-paired.cwl

Branch/Commit ID: caea457
workflow graph mutect panel-of-normals workflow

https://github.com/fgomez02/analysis-workflows.git

Path: definitions/pipelines/panel_of_normals.cwl

Branch/Commit ID: No_filters_detect_variants
workflow graph wf_get_itrdb_data.cwl

https://github.com/idaks/cwl_modeling.git

Path: yw_cwl_modeling/yw2cwl_parser/example_sql/get_itrdb_data/wf_get_itrdb_data.cwl

Branch/Commit ID: master
workflow graph ChIP-exo peak caller workflow for single-end samples with no P-Value inflection

This workflow execute peak caller and QC from ChIP-exo for single-end samples with no P-Value inflection

 https://gitlab.com/r78v10a07/cwl-workflow.git

Path: workflows/ChIP-exo/peak_caller-SE-no_inflection.cwl

Branch/Commit ID: master
workflow graph Whole Genome Sequence processing workflow scattered over samples

<p>This is a “real-world” workflow example for processing Next Generation Sequencing (NGS) Whole Genome Sequence (WGS) data.</p> <p>You can learn more and run this workflow yourself by going through the <a href=\"https://doc.arvados.org/main/user/tutorials/wgs-tutorial.html\">Processing Whole Genome Sequences</a> walkthrough in the Arvados user guide.</p> <p>The steps of this workflow include:</p> <ol> <li>Check of fastq quality using FastQC</li> <li>Local alignment using BWA-MEM</li> <li>Variant calling in parallel using GATK Haplotype Caller</li> <li>Generation of an HTML report comparing variants against ClinVar archive</li> </ol> <p>The primary input parameter is the <b>Directory of paired FASTQ files</b>, which should contain paired FASTQ files (suffixed with _1 and _2) to be processed. The workflow scatters over the samples to process them in parallel.</p> <p>The remaining parameters are reference data used by various tools in the pipeline.</p>

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/wgs-processing-wf.cwl

Branch/Commit ID: main
workflow graph wf_trim_and_map_chimeric_se.cwl

This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment

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

Path: cwl/wf_trim_and_map_chimeric_se.cwl

Branch/Commit ID: master
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/aml_trio_cle_gathered.cwl

Branch/Commit ID: downsample_and_recall
workflow graph cmsearch-multimodel.cwl

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

Path: workflows/cmsearch-multimodel.cwl

Branch/Commit ID: d4e5e53