Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-wf4.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf4.cwl

Branch/Commit ID: f207d168f4e7eb4dd2279840d4062ba75d9c79c3

Packed ID: main
workflow graph Filter DiffBind results for deepTools heatmap analysis

Filter DiffBind results for deepTools heatmap analysis ====================================================== Filter differentially bound sites from DiffBind analysis to be used with deepTools heatmap analysis

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

Path: workflows/filter-diffbind-for-heatmap.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph count-lines4-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines4-wf.cwl

Branch/Commit ID: f207d168f4e7eb4dd2279840d4062ba75d9c79c3
workflow graph super-enhancer.cwl

Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: e706ffe742cfdf713c4315ab2fb56d07f7e688cb
workflow graph scatter-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf1.cwl

Branch/Commit ID: 5ae5798f1c0c8d2178986b77cfd74edff510877a
workflow graph annotate.cwl

https://github.com/hubmapconsortium/hra-workflows.git

Path: steps/annotate.cwl

Branch/Commit ID: 3dfea9ce19138c930dec92024496c4814a290f12
workflow graph count-lines7-wf_v1_0.cwl

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

Path: testdata/count-lines7-wf_v1_0.cwl

Branch/Commit ID: 039be8fe42daf65a3fc926af47e90ac975d02062
workflow graph rnaseq-se-dutp.cwl

Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.

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

Path: workflows/rnaseq-se-dutp.cwl

Branch/Commit ID: e706ffe742cfdf713c4315ab2fb56d07f7e688cb
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: 87f213456b3f966b773d396cce1fe5a272dad858
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa