Explore Workflows

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Graph Name Retrieved From View
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

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

Path: workflows/bwa-index.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb
workflow graph Single-Cell RNA-Seq Trajectory Analysis

Single-Cell RNA-Seq Trajectory Analysis Infers developmental trajectories and pseudotime from cells clustered by similarity of gene expression data.

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

Path: workflows/sc-rna-trajectory.cwl

Branch/Commit ID: 93b844a80f4008cc973ea9b5efedaff32a343895
workflow graph LBA_calibrator.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/LBA_calibrator.cwl

Branch/Commit ID: efd84bf3c56117c6a05852b3b47aaf4ad8de11bd
workflow graph Identifies non-coding RNAs using Rfams covariance models

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/assembly/cmsearch-multimodel-assembly.cwl

Branch/Commit ID: 6ec8d032feb120eb0eebf9a0c01d48deabf42eea
workflow graph ST520113.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: ST520113.cwl

Branch/Commit ID: 272db37d2b8108a146769f0fb0383bb824c9788f
workflow graph WF5201.cwl

https://github.com/Marco-Salvi/dtc51.git

Path: WF5201.cwl

Branch/Commit ID: 272db37d2b8108a146769f0fb0383bb824c9788f
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: 93b844a80f4008cc973ea9b5efedaff32a343895
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-noscreen-fastq.workflow.cwl

Branch/Commit ID: 091374dc59a23966338638a668ae397d4ee20b2f
workflow graph trim-chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-chipseq-pe.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6