Explore Workflows

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

Graph Name Retrieved From View
workflow graph blastp_wnode_struct

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

Path: task_types/tt_blastp_wnode_struct.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph count-lines10-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph xenbase-rnaseq-se.cwl

XenBase workflow for analysing RNA-Seq single-end data

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

Path: workflows/xenbase-rnaseq-se.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph count-lines6-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines6-wf.cwl

Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda
workflow graph 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 **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 282762f8bbaea57dd488115745ef798e128bade1
workflow graph Super-enhancer post ChIP-Seq analysis

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: 2b8146f76595f0c4d8bf692de78b21280162b1d0
workflow graph umi duplex alignment fastq workflow

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

Path: definitions/pipelines/umi_duplex_alignment.cwl

Branch/Commit ID: 1560e7817fdb71d58aca7f98aba68809d840ade1
workflow graph count-lines8-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca