Explore Workflows

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 18b8fdf7d425d8e7d8986e08904ef09492798cf6

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 875b928ce50a3202f5954843b79ea86683c160fa

Packed ID: main

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: 5bdb3d3dd47d8d1b3a1685220b4b6ce0f94c055e

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

Path: tests/timelimit2-wf.cwl

Branch/Commit ID: 6397014050177074c9ccd0d771577f7fa9f728a3

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: 6bfb64375e7ebb6eb40f463ede86d8deccdb9eff

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

Path: definitions/pipelines/umi_duplex_alignment.cwl

Branch/Commit ID: 479c9b3e3fa32ec9c7cd4073cfbccc675fd254d9

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