Explore Workflows

This is a workflow to go from standard bams to collapsed bams and QC results.

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

Path: workflows/subworkflows/standard_bam_to_collapsed_qc.cwl

Branch/Commit ID: master

https://github.com/h3abionet/h3agatk.git

Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-snp.cwl

Branch/Commit ID: 1.0.1

https://github.com/dockstore/hello_world.git

Path: hello_world.cwl

Branch/Commit ID: master

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/functional_analysis.cwl

Branch/Commit ID: 5e82174

https://github.com/cancerit/workflow-seq-import.git

Path: cwls/chksum_xam_to_interleaved_fq.cwl

Branch/Commit ID: 0.4.1

https://github.com/genome/cancer-genomics-workflow.git

Path: unaligned_bam_to_bqsr/align.cwl

Branch/Commit ID: toil_compatibility

https://github.com/azzaea/tsts.git

Path: cwl/host.sort.workflow.cwl

Branch/Commit ID: master

This demonstrates how to wrap a \"real\" workflow with a checker workflow that runs both the tool and a tool that performs verification of results

https://github.com/dockstore-testing/dockstore-workflow-md5sum-unified.git

Path: checker_workflow_wrapping_workflow.cwl

Branch/Commit ID: 1.3.0

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 0cd2d70

This workflow takes the PeptideProphet, and the ProteinProphet output files, and applies a stringent False Discovery Rate (FDR) filtering. Peptide and proteins are filtered individually at 1% FDR. The high-quality PSMs, peptides, and proteins are then quantified using a label-free algorithm that uses the apex peak intensity as a measurement. Finally, the isobaric tags are quantified and annotated with the correct sample labels.

https://github.com/cwl-apps/fragpipe-proteomics-pipeline-tutorial.git

Path: FragPipe-Filter-Quant-Report/fragpipe-filter-quant-report.cwl

Branch/Commit ID: main