Explore Workflows

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

Graph Name Retrieved From View
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: c17cac4c046f8ba2b8574a121c44a72d2e6b27e6
workflow graph rna amplicon analysis for fasta files

RNAs - qc, preprocess, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/amplicon-fasta.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f
workflow graph Seurat for comparative scRNA-seq analysis of across experimental conditions

Runs Seurat for comparative scRNA-seq analysis of across experimental conditions ================================================================================

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

Path: workflows/seurat-cluster.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f
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: ddc35c559d1ac6aab4972fe1a2b63300c4373f54
workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: a2d6cd4c53bf3501f6bd79edebb7ca30bba8456f
workflow graph Bacterial Annotation, pass 1, genemark training, by HMMs (first pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass1.cwl

Branch/Commit ID: 5463361069e263ad6455858e054c1337b1d9e752
workflow graph DESeq2 Multi-factor Analysis

DESeq2 Multi-factor Analysis Runs DeSeq2 multi-factor analysis with manual control over major parameters

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

Path: workflows/deseq-multi-factor.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf
workflow graph sec-wf-out.cwl

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca
workflow graph Tag enrichment heatmap and density profile around regions of interest

Generates tag density heatmap and histogram for the centered list of features in a headerless regions file. - If provided regions file is a gene list with the following columns `chrom start end name score strand` set `Gene TSS` as a re-centering criteria. - If provided regions file is a peak list with the following columns `chrom start end name` set `Peak Center` as a re-centering criteria. `score` column is always ignored.

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

Path: workflows/heatmap.cwl

Branch/Commit ID: cc6fa135d04737fdde3b4414d6e214cf8c812f6e