Explore Workflows

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

Graph Name Retrieved From View
workflow graph TAP

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

Path: CWL/Workflows/tap.prok.workflow.cwl

Branch/Commit ID: 735a989b6923e9207baace2702be4554d70c92d7
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 89098668413e90519c99b35143bffec509d3599c
workflow graph Generate genome index bowtie

Workflow makes indices for [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016). Executes `bowtie-index` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a directory

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

Path: workflows/bowtie-index.cwl

Branch/Commit ID: 9b4dc225c537685b9c9a32d931d3892d20953dd7
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 89098668413e90519c99b35143bffec509d3599c
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: be32f1363f9a9a9247d738e9593b207e9c5172c8
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: ef7f3345b352319ec22dffba26c79df033b141f9
workflow graph step-valuefrom3-wf_v1_0.cwl

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

Path: testdata/step-valuefrom3-wf_v1_0.cwl

Branch/Commit ID: 124a08ce3389eb49066c34a4163cbbed210a0355
workflow graph Trim Galore RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow must be used with paired-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 4. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 2 (after running STAR) 5. Generate BigWig file using sorted BAM file 6. Map input FASTQ files 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/trim-rnaseq-pe.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
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: 9b4dc225c537685b9c9a32d931d3892d20953dd7