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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: ba3ff09328cc646d7254b2d2ee0fbe1abca3d4ad

Single-cell Multiome ATAC and RNA-Seq Analyze Runs filtering, normalization, scaling, integration (optionally) and clustering for a single or aggregated single-cell Multiome ATAC and RNA-Seq datasets.

https://github.com/Barski-lab/sc-seq-analysis.git

Path: workflows/sc-multiome-analyze-wf.cwl

Branch/Commit ID: 9064af1cdd8e97bcdf4473e2a741e1ada1a7c4f3

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/emg-pipeline-v3.cwl

Branch/Commit ID: 3f85843d4a6debdabe96bc800bf2a4efdcda1ef3

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-Seq/chip-seq-alignment.cwl

Branch/Commit ID: 793e327acc1d159ff601043ee88651fca62350dd

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/datirium/workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: c0543fc3f552a521aa498b6597b9a972599de056

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/record-output-wf.cwl

Branch/Commit ID: 5f27e234b4ca88ed1280dedf9e3391a01de12912

Workflow to merge a large number of maf files into a single consensus maf file for use with GetBaseCountsMultiSample

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

Path: cwl/consensus_maf.cwl

Branch/Commit ID: 2e1a01a788126f2901ffecc92a48fcbcb81776e1

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/subworkflows/bwa_mem.cwl

Branch/Commit ID: a4a3547b9790e99a58424a0dfcb4e467a7691d6a

https://github.com/datirium/workflows.git

Path: metadata/chipseq-header.cwl

Branch/Commit ID: 2005c6b7f1bff6247d015ff6c116bd9ec97158bb

https://github.com/ding-lab/TinDaisy.git

Path: cwl/workflows/tindaisy-vep_annotate.cwl

Branch/Commit ID: c81058f1f039446ab10488699675a42129040ecd