Explore Workflows

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff

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: 5cad957fec135aa55ca8d588372db0557ca1cad5

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

Path: definitions/pipelines/gathered_downsample_and_recall.cwl

Branch/Commit ID: 39ac49f5d080bbb6bfa97246f46a5b621254f622

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open otus and assigns taxa using greengenes. The output are taxa plots.

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

Path: CWL/Workflows/qiime/cluster2plot.cwl

Branch/Commit ID: ea3f99c0fc58d161e068bd5077c362768e534b92

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

Path: workflows/phaseup-concat.cwl

Branch/Commit ID: d77bb56f954217d3ba2aae801f1a08470b0793df

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

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: a28a8077a8c4dbf117d16799807483a2532af3f3

https://git.astron.nl/eosc/prefactor3-cwl.git

Path: workflows/LBA_target.cwl

Branch/Commit ID: 16b52facea91f7ebd2200c471b69a8c6a49b9e66

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

Path: testdata/md5sum_v11.cwl

Branch/Commit ID: 02d6dbd3d48d50adfd4afb1f7d92e8a4284bcab9

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

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 8b0cacc5510eb3eed4e6d6db4bb844cc6114b1dc

https://git.astron.nl/eosc/prefactor3-cwl.git

Path: workflows/HBA_target.cwl

Branch/Commit ID: f4d9e23e09d2ab8dc266e3d9e164709e5c0f2a13