Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
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: 45604eaeea15030c7302941c761464ce392abf74 |
|
|
|
Spectral_counting_workflow.cwl
|
https://github.com/adamscharlotte/CWL-workflow.git
Path: Spectral_counting_workflow.cwl Branch/Commit ID: f165c14d6d2e20a5133fc42251ae565fcbe520f6 |
|
|
|
Vcf concordance evaluation workflow
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/vcf_eval_concordance.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
|
|
|
bgzip and index VCF
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/bgzip_and_index.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
|
|
|
ROSE: rank ordering of super-enhancers
Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff) |
https://github.com/datirium/workflows.git
Path: workflows/super-enhancer.cwl Branch/Commit ID: 3d280a2a4b4f1560f56991086f712fa22ddc3364 |
|
|
|
samtools_view_sam2bam
|
https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git
Path: structuralvariants/cwl/subworkflows/samtools_view_sam2bam.cwl Branch/Commit ID: 9ac2d150a57d1996210ed6a44dd0c0404dab383c |
|
|
|
Subworkflow to allow calling different SV callers which require bam files as inputs
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479 |
|
|
|
Unaligned bam to sorted, markduped bam
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/align_sort_markdup.cwl Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a |
|
|
|
Apply filters to VCF file
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/filter_vcf_mouse.cwl Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d |
|
|
|
Subworkflow to allow calling different SV callers which require bam files as inputs
|
https://github.com/genome/analysis-workflows.git
Path: definitions/subworkflows/single_sample_sv_callers.cwl Branch/Commit ID: 788bdc99c1d5b6ee7c431c3c011eb30d385c1370 |
