Explore Workflows

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

Graph Name Retrieved From View
workflow graph Interval overlapping alignments counts

Interval overlapping alignments counts ====================================== Reports the count of alignments from multiple samples that overlap specific intervals.

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

Path: workflows/bedtools-multicov.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph multiome pipeline using Salmon and Alevin (HuBMAP scRNA-seq pipeline) and HuBMAP scATAC-seq pipeline

https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git

Path: pipeline.cwl

Branch/Commit ID: c338cd390c994eb3601cc7749878add1056953ba
workflow graph Genomic regions intersection and visualization

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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

Path: workflows/intervene.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph count-lines7-wf_v1_2.cwl

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

Path: testdata/count-lines7-wf_v1_2.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph scatter-wf2_v1_0.cwl

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

Path: testdata/scatter-wf2_v1_0.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph map medium and long reads (> 100 bp) against reference genome

https://github.com/common-workflow-library/bio-cwl-tools.git

Path: bwa/BWA-Mem2-single.cwl

Branch/Commit ID: 1bfe9fc07978c8463399eec690798effb8431c35
workflow graph scatter-wf1_v1_0.cwl

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

Path: testdata/scatter-wf1_v1_0.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph count-lines7-wf_v1_0.cwl

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

Path: testdata/count-lines7-wf_v1_0.cwl

Branch/Commit ID: 8058c7477097f90205dd7d8481781eb3737ea9c9
workflow graph Cell Ranger Count (RNA+ATAC)

Cell Ranger Count (RNA+ATAC) Quantifies single-cell gene expression and chromatin accessibility of the sequencing data from a single 10x Genomics library in a combined manner. The results of this workflow are primarily used in either “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” or “Cell Ranger Aggregate (RNA+ATAC)” pipelines.

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

Path: workflows/cellranger-arc-count.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Cell Ranger Count (RNA)

Cell Ranger Count (RNA) Quantifies single-cell gene expression of the sequencing data from a single 10x Genomics library. The results of this workflow are primarily used in either “Single-Cell RNA-Seq Filtering Analysis” or “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines.

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16