Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph Example of setting up a simulation system

Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

https://github.com/stain/biobb_example_workflow.git

Path: protein_md.cwl

Branch/Commit ID: master
workflow graph Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph module-6

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-6.cwl

Branch/Commit ID: 2.4.x
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: downsample_and_recall
workflow graph module-1

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/module-1.cwl

Branch/Commit ID: dev
workflow graph germline-gpu-v4.2.1.cwl

https://github.com/NCGM-genome/WGSpipeline.git

Path: Workflows/germline-gpu-v4.2.1.cwl

Branch/Commit ID: main
workflow graph count-lines15-wf.cwl

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

Path: tests/count-lines15-wf.cwl

Branch/Commit ID: main
workflow graph harmonization_bwa_mem_prod.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/harmonization_bwa_mem_prod.cwl

Branch/Commit ID: master
workflow graph adapter for sequence_align_and_tag

Some workflow engines won't stage files in our nested structure, so parse it out here

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

Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl

Branch/Commit ID: master
workflow graph samples_fillout_index_batch_workflow.cwl

Wrapper to run bam indexing on all bams before submitting for samples fillout Also includes steps to pre-filter some maf input files NOTE: each sample in a sample_group must have a .bam file, and there must be a minumum of 1 .maf file amoungst samples in the same sample_group this means that for each sample in the sample_group, a .bam is required but a .maf is optional as long as one sample in the group has a .maf this also means that singleton sample groups, or a sample group with only one sample, MUST include a .maf file; singletons cannot lack a .maf NOTE: all .maf files must be valid, at a minimum they must have a header and at least one variant if a sample has no variants in its .maf file, or has an empty .maf file, then it should NOT have a maf_file entry associated with it

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

Path: cwl/samples_fillout_index_batch_workflow.cwl

Branch/Commit ID: master