Explore Workflows

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/datirium/workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 9e3c3e65c19873cd1ed3cf7cc3b94ebc75ae0cc5

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: d8a8af9fdb69c0a4003680c1d3b96f35d5e48f0e

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 9362082213e20315f76f6f5c235cac3aae565747

https://github.com/reanahub/reana-demo-worldpopulation.git

Path: workflow/cwl/worldpopulation-htcondorcern.cwl

Branch/Commit ID: 379334455b663b295a61a0ec057bfc080f9c7c6e

Quality Control and Raw Data trimming

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/trimmed_fastq.cwl

Branch/Commit ID: 5cc8306ce84c027db4c092077983294557213136

https://github.com/Andreja28/cloud-workflows.git

Path: cwl/torso/workflow.cwl

Branch/Commit ID: b2d5b67c9bbc0cce97dcf65f3cdc8da2c156e145

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-blast-clustalo-phylogeny.cwl

Branch/Commit ID: 5df6b762980b15b0f6389149311b82bdd6dff37d

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

Path: src/test/resources/cwl/lobstr-v1/lobSTR-workflow.cwl

Branch/Commit ID: 1282d7530484390dfed25a9c4e6cfa925353172c

CNV GRIDSS calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_gridss.cwl

Branch/Commit ID: 5cc8306ce84c027db4c092077983294557213136

CNV Manta calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_manta.cwl

Branch/Commit ID: 5cc8306ce84c027db4c092077983294557213136