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workflow graph workflow.cwl

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: 3bc4fab5503e58521ed0eb9c0d035ac18460dc13
workflow graph Execute CRISPR

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

Path: bacterial_mobile_elem/wf_bacterial_mobile_elem.cwl

Branch/Commit ID: ed27a47e80a85c76cb7285a78965d59537f79f10
workflow graph canine_add_matched_rna.cwl

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_add_matched_rna.cwl

Branch/Commit ID: 7da5645975f5712362cce7908d2ab138e05876fb
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 4e7b8f243f5356653edd286eab24f419f39da189
workflow graph Prepare user input

Prepare user input for NCBI-PGAP pipeline

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

Path: prepare_user_input2.cwl

Branch/Commit ID: 68b828ac482956a03325623d817780986f34fb31
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: 68b828ac482956a03325623d817780986f34fb31
workflow graph record-output-wf_v1_2.cwl

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

Path: testdata/record-output-wf_v1_2.cwl

Branch/Commit ID: ed26684328ca370c247f549166f3edcb14a2f9e0
workflow graph nestedworkflows.cwl

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

Path: src/_includes/cwl/workflows/nestedworkflows.cwl

Branch/Commit ID: 6d2bd4ed2225cd52e0e3b7da8f22dee1c6ca091b
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: ed27a47e80a85c76cb7285a78965d59537f79f10
workflow graph HelloWorld-pipeline-020.cwl#hello_pipeline

https://github.com/ILIAD-ocean-twin/application_package.git

Path: HelloWorld/files/HelloWorld-pipeline-020.cwl

Branch/Commit ID: 08ed13b4a9d0e5a726e100a0a9989383fd07cea1

Packed ID: hello_pipeline