Explore Workflows

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Graph Name Retrieved From View
workflow graph WGS QC workflow mouse

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

Path: definitions/subworkflows/qc_wgs_mouse.cwl

Branch/Commit ID: c6bbd4cdd612b3b5cc6e9000df4800c21e192bf5
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Genelists heatmap - RNA-seq expression data visualized

# Genelists heatmap - RNA-seq expression data visualized This visualization workflow takes as input 1 or more genelists derived from the DESeq and/or diffbind workflows along with user-selected samples and visualizes RNA-Seq expression data in a single morpheus heatmap. ### __References__ - Morpheus, https://software.broadinstitute.org/morpheus

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

Path: workflows/genelists-deseq-only.cwl

Branch/Commit ID: fa4f172486288a1a9d23864f1d6962d85a453e16
workflow graph Single-Cell ATAC-Seq Dimensionality Reduction Analysis

Single-Cell ATAC-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of chromatin accessibility data from the outputs of “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell ATAC-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.

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

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph WGS and MT analysis for fastq files

rna / protein - qc, preprocess, filter, annotation, index, abundance

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

Path: CWL/Workflows/wgs-fastq.workflow.cwl

Branch/Commit ID: f906212e2c9a88280ae36545e5422f25752aa8f4
workflow graph RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: 4dcc405133f22c63478b6091fb5f591b6be8950f
workflow graph count-lines5-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines5-wf.cwl

Branch/Commit ID: 48bd6c751aceef30614d9e43d91865980035781f
workflow graph count-lines1-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines1-wf-noET.cwl

Branch/Commit ID: a0f2d38e37ff51721fdeaf993bb2ab474b17246b
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: a2d6cd4c53bf3501f6bd79edebb7ca30bba8456f
workflow graph env-wf3.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf3.cwl

Branch/Commit ID: a3d565bf8e630101d25d31804cfbceb0a0ba28de