Explore Workflows
View already parsed workflows here or click here to add your own
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make_final_outputs_workflow.cwl
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https://github.com/NCI-GDC/gdc-rnaseq-cwl.git
Path: rnaseq-star-align/subworkflows/rnaseq_processing/make_final_outputs_workflow.cwl Branch/Commit ID: 1da226915d882b79996bae7ca05eae0b3dcbf272 |
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msi_workflow.cwl
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: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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download_gtf.cwl
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https://github.com/yyoshiaki/VIRTUS2.git
Path: workflow/download_gtf.cwl Branch/Commit ID: e4f95cc3bd7bbe0d4018b0471bddafe97ceaed0c |
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docker_VisIVO_ImpView_Workflow.cwl
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https://github.com/VisIVOLab/VisIVOCWL.git
Path: docker_VisIVO_ImpView_Workflow.cwl Branch/Commit ID: dec55ecc719526a09b91de40993930b9a14c21fc |
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portal-workflow.cwl
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https://github.com/mskcc/pluto-cwl.git
Path: cwl/portal-workflow.cwl Branch/Commit ID: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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Detect Variants workflow
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/detect_variants.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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exome alignment with qc
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https://github.com/genome/analysis-workflows.git
Path: definitions/pipelines/exome_alignment.cwl Branch/Commit ID: ae79bc51e8b502164dbe74ea3b068d6d4d36a1f8 |
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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_sv.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_sv.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: 59b69eed7ffefcffd81313ec8ffb84c0d716b933 |
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VIRTUS.PE.cwl
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https://github.com/yyoshiaki/VIRTUS2.git
Path: workflow/VIRTUS.PE.cwl Branch/Commit ID: e4f95cc3bd7bbe0d4018b0471bddafe97ceaed0c |
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Subworkflow to allow calling different SV callers which require bam files as inputs
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https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46 |
