Explore Workflows

https://git.astron.nl/RD/VLBI-cwl.git

Path: workflows/concatenate-flag.cwl

Branch/Commit ID: fdafca28275be6206bd8dbe49866c7e46c2d4dc1

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

Path: tests/wf/1st-workflow.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b

Workflow to run GetBaseCountsMultiSample fillout on a number of samples, each with their own bam and maf files

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

Path: cwl/igv-report_maf_workflow.cwl

Branch/Commit ID: e19ef998e906eb915cf4351a3599abd9bff57205

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

Path: cwl/analysis-workflow.cwl

Branch/Commit ID: ab0192b19d01046d5db2fc5233678a97b47210e6

run diamond on mutlple DBs and merge-sort results

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-diamond.workflow.cwl

Branch/Commit ID: 721aaf285e1848c3c52da38a1fed95192aeff8f4

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort_datetime.cwl

Branch/Commit ID: 8949fc2d68efe128ce841739d1190645dbd233bb

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

Path: definitions/pipelines/bisulfite.cwl

Branch/Commit ID: 37a3622d1d03812e4f868b5024c52607696bfb75

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: 09dd29d3ceebae28fc7c00ad5d91627705a6b0b9

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: 2a88d5c2d139ff817b21b480ccf9c1cd7139b00c

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

Path: testdata/workflow_input_format_expr_v1_2.cwl

Branch/Commit ID: 6a46105708870aa3cf97c8ba91884272b2857975