Explore Workflows

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

Graph Name Retrieved From View
workflow graph SoupX (workflow) - an R package for the estimation and removal of cell free mRNA contamination

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

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

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph ROSE: rank ordering of super-enhancers

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph createindex_singlevirus.cwl

https://github.com/yyoshiaki/VIRTUS.git

Path: workflow/createindex_singlevirus.cwl

Branch/Commit ID: 16dbe9d99137cbfee834fc22b79190f812543f7e
workflow graph AltAnalyze CellHarmony

AltAnalyze CellHarmony ======================

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

Path: workflows/altanalyze-cellharmony.cwl

Branch/Commit ID: 581156366f91861bd4dbb5bcb59f67d468b32af3
workflow graph wf-variantcall.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: NA12878-chr20/NA12878-platinum-chr20-workflow/wf-variantcall.cwl

Branch/Commit ID: af9a5621efcb44c249697d6df071fe4defe389ac
workflow graph wf-alignment.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: NA12878-chr20/NA12878-platinum-chr20-workflow/wf-alignment.cwl

Branch/Commit ID: af9a5621efcb44c249697d6df071fe4defe389ac
workflow graph somatic_exome: exome alignment and somatic variant detection

somatic_exome is designed to perform processing of mutant/wildtype H.sapiens exome sequencing data. It features BQSR corrected alignments, 4 caller variant detection, and vep style annotations. Structural variants are detected via manta and cnvkit. In addition QC metrics are run, including somalier concordance metrics. example input file = analysis_workflows/example_data/somatic_exome.yaml

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph scatter2.cwl

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: 07ebbea2bdf97955060c1dd563580b386388519b
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: 60854b5d299df91e135e05d02f4be61f6a310fbc