Explore Workflows

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

Graph Name Retrieved From View
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: 549fac35bf6b8b1c25af0f4f6c3f162c40dc130e
workflow graph strelka workflow

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

Path: definitions/subworkflows/strelka_and_post_processing.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: d218e081d8f6a4fdab56a38ce0fc2fae6216cecc
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: detect_variants/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 31602b94b34ff55876147c7299e1bec47e8d1a31
workflow graph Generate genome indices for STAR & bowtie

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 00ea05e22788029370898fd4c17798b11edf0e57
workflow graph MEME motif

This workflow uses MEME suite for motif finding

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-Seq/meme-motif.cwl

Branch/Commit ID: 7364aa3799fd3bd7584049228618301bda53a3af
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 50d161364e2859ed5c95ef07c9f7234f1431cf31
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: be32f1363f9a9a9247d738e9593b207e9c5172c8
workflow graph Single-Cell ATAC-Seq Differential Accessibility Analysis

Single-Cell ATAC-Seq Differential Accessibility Analysis Identifies differentially accessible regions between any two groups of cells, optionally aggregating chromatin accessibility data from single-cell to pseudobulk form.

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

Path: workflows/sc-atac-dbinding.cwl

Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e