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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: 45604eaeea15030c7302941c761464ce392abf74

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: 2a922ab11b2f9c21ae4955c74563543b87717b93

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

Path: tests/wf/js_output_workflow.cwl

Branch/Commit ID: cb81b22abc52838823da9945f04d06739ab32fda

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_readgroup_fastq_se_http.cwl

Branch/Commit ID: 0d3fdddeae5a398e476d91aa98766965866d8eae

Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/rnaseq-pe.cwl

Branch/Commit ID: 9a03dbe8829ca649814d9c8bd11fe3a673750a95

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

Path: workflows/facet_subtract.cwl

Branch/Commit ID: b4c18092637726b245f7040d87fbfdf7baee3e8e

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/conflict-wf.cwl

Branch/Commit ID: 6397014050177074c9ccd0d771577f7fa9f728a3

Packed ID: collision

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

Path: testdata/scatter-wf2_v1_0.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 70e05adeda8b3b4c77b8947266684ce4305db6ac

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: baefdcb58fcc76e3378cf705fc6a3e69ef35bb47