Explore Workflows

Workflow to run the MSI analysis on a batch of samples

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

Path: cwl/msi_workflow.cwl

Branch/Commit ID: e19ef998e906eb915cf4351a3599abd9bff57205

https://github.com/adamscharlotte/CWL-workflow.git

Path: SARS_psm_workflow.cwl

Branch/Commit ID: fad08b1bff0ae38dca3a39907b25a248d069e514

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

Path: tests/wf/sec-wf.cwl

Branch/Commit ID: e414985ecf9a371c5834e76cdb12ef9619893276

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

Path: tests/count-lines18-wf.cwl

Branch/Commit ID: 6397014050177074c9ccd0d771577f7fa9f728a3

https://github.com/vavien/bi-cwl.git

Path: secondary_sqrt_workflow.cwl

Branch/Commit ID: main

https://github.com/andreja28/cloud-workflows.git

Path: cwl/bone-min-org-app/workflow.cwl

Branch/Commit ID: master

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

Path: vecscreen/vecscreen.cwl

Branch/Commit ID: aa64bf6a90e0780ab564de865dbb027df98c0a01

CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files 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 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 └── 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.cwl

Branch/Commit ID: c10d8bcf045067b3510bff68e2e957fccea0d7ea

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

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: 68311dd5328bf6b782a370a0253b41062a3359a3

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/dnaseq/mixed_library_metrics.cwl

Branch/Commit ID: b2f7a697e08220234062a9cf558ba169d255b4a4