Explore Workflows

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

Graph Name Retrieved From View
workflow graph Detect Docm variants

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph Apply filters to VCF file

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph mpi_simple_wf.cwl

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: 6c86caa0571fd186d90a6600e0bb405596d4a5e0
workflow graph Run taxonomic classification, create OTU table and krona visualisation

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/classify-otu-visualise.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea
workflow graph exome alignment and germline variant detection, with optitype for HLA typing

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

Path: definitions/pipelines/germline_exome_hla_typing.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c
workflow graph default-dir5.cwl

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

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23
workflow graph Build Bismark indices

Copy fasta_file file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph Single-Cell RNA-Seq Filtering Analysis

Single-Cell RNA-Seq Filtering Analysis Removes low-quality cells from the outputs of the “Cell Ranger Count (RNA)”, “Cell Ranger Count (RNA+VDJ)”, and “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines. The results of this workflow are used in the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline.

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

Path: workflows/sc-rna-filter.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: 424a01693259a75641dc249d553235aa38a6ce23