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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: 2a88d5c2d139ff817b21b480ccf9c1cd7139b00c

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

Path: cwl/concat.cwl

Branch/Commit ID: 2a88d5c2d139ff817b21b480ccf9c1cd7139b00c

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 17268d1493d9e558113b2c35c0be6b3fb961b2a3

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

Path: bacterial_ncrna/wf_gcmsearch.cwl

Branch/Commit ID: 192b813eed8c0d368e69057cb39415175dd15128

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

Path: workflows/facet_subtract.cwl

Branch/Commit ID: a58fba4c1343bed66a5b47ea6a197b0385dfd39a

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

Path: workflows/HBA_target_VLBI.cwl

Branch/Commit ID: 0c5bd78e3f2d08564f5c9a563bcc8bb7704e6202

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/modules/maf-processing.cwl

Branch/Commit ID: 75010576d1cd99d6e3572e32fd2dabbb0f1bb8f3

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 295e7b7f51727c0f2d6cc86ce817449b2e8dba3c

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: 6d2998467fada81e5024c1f8594ae167514cb290

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

Path: testdata/step-valuefrom2-wf_v1_0.cwl

Branch/Commit ID: 917a880e3a48c2ea7da10aeae20f9a03fb1c6a62