Explore Workflows

https://github.com/arvados/arvados-tutorial.git

Path: WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl

Branch/Commit ID: main

CWL workflow for generating Roslin / Argos post pipeline analysis files and cBioPortal data and metadata files This workflow includes Facets and Facets Suite usages 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 pairs 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 ├── facets │ ├── <tumor_id>.<normal_id> (passed) │ │ └── <facets_files> │ └── <tumor_id>.<normal_id> (failed) │ └── <log_files> └── 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_sv.txt ├── data_fusions.txt ├── data_mutations_extended.txt ├── meta_clinical_patient.txt ├── meta_clinical_sample.txt ├── meta_CNA.txt ├── meta_sv.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_with_facets.cwl

Branch/Commit ID: master

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: master

Remove reads from fasta files based on sequence stats. Return fasta files with reads passed and reads removed.

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/preprocess-fasta.workflow.cwl

Branch/Commit ID: master

This workflow aligns the fastq files using magicblast for paired-end samples

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

Path: workflows/Alignments/magicblast-alignment.cwl

Branch/Commit ID: master

Single-Cell RNA-Seq Differential Expression Analysis Identifies differentially expressed genes between any two groups of cells, optionally aggregating gene expression data from single-cell to pseudobulk form.

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

Path: workflows/sc-rna-de-pseudobulk.cwl

Branch/Commit ID: master

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/module-2.cwl

Branch/Commit ID: master

GATK4.1.2 Calculate tumor-normal contamination workflow

https://github.com/NCI-GDC/gatk4_mutect2_cwl.git

Path: subworkflows/calculate_contamination_workflow.cwl

Branch/Commit ID: master

This CWL workflow outlines the steps for setting up and executing an experiment based on objectives, SOP references, parameters, and experimental design. Version: 1.0 Description: Workflow for executing and tracking experiments. Includes validation and logging steps.

https://github.com/pascmont/cwltest.git

Path: myAIWorkflow3.cwl

Branch/Commit ID: main

rna / protein - qc, preprocess, filter, annotation, index, abundance

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/wgs-noscreen-fasta.workflow.cwl

Branch/Commit ID: master