Explore Workflows

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

Graph Name Retrieved From View
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff
workflow graph count-lines8-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl

Branch/Commit ID: bffea7fd5e864c5221c13a815d00d0a2fad178cc
workflow graph gcaccess_from_list

https://github.com/ncbi/pgap.git

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 681555881cbdf95a1f4c29f6dc272eb6ca8e4d60
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: d297528e53b6c1ecb69b1ab27b8e03323b4463ad
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622
workflow graph Per-chromosome pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 70e05adeda8b3b4c77b8947266684ce4305db6ac
workflow graph md5sum.cwl

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

Path: testdata/md5sum.cwl

Branch/Commit ID: afc644e143c697aefc006e7b94bc460e594fc588
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff
workflow graph workflow_with_facets.cwl

CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files This workflow includes Facets and Facets Suite usages Inputs ------ The following parameters are required: project_id project_pi request_pi project_short_name project_name project_description cancer_type cancer_study_identifier argos_version_string helix_filter_version is_impact extra_pi_groups pairs The following filenames are required: analysis_mutations_filename analysis_gene_cna_filename analysis_sv_filename analysis_segment_cna_filename cbio_segment_data_filename cbio_meta_cna_segments_filename The following filenames have default values and are optional: cbio_mutation_data_filename cbio_cna_data_filename cbio_fusion_data_filename cbio_clinical_patient_data_filename cbio_clinical_sample_data_filename cbio_clinical_sample_meta_filename cbio_clinical_patient_meta_filename cbio_meta_study_filename cbio_meta_cna_filename cbio_meta_fusions_filename cbio_meta_mutations_filename cbio_cases_all_filename cbio_cases_cnaseq_filename cbio_cases_cna_filename cbio_cases_sequenced_filename Output ------ Workflow output should look like this: output ├── analysis │   ├── <project_id>.gene.cna.txt │   ├── <project_id>.muts.maf │   ├── <project_id>.seg.cna.txt │   └── <project_id>.svs.maf ├── facets │ ├── <tumor_id>.<normal_id> (passed) │ │ └── <facets_files> │ └── <tumor_id>.<normal_id> (failed) │ └── <log_files> └── portal ├── case_list │   ├── cases_all.txt │   ├── cases_cnaseq.txt │   ├── cases_cna.txt │   └── cases_sequenced.txt ├── data_clinical_patient.txt ├── data_clinical_sample.txt ├── data_CNA.ascna.txt ├── data_CNA.scna.txt ├── data_CNA.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_fusions.txt ├── meta_mutations_extended.txt ├── meta_study.txt ├── <project_id>_data_cna_hg19.seg └── <project_id>_meta_cna_hg19_seg.txt

https://github.com/mskcc/pluto-cwl.git

Path: cwl/workflow_with_facets.cwl

Branch/Commit ID: 5cad957fec135aa55ca8d588372db0557ca1cad5