Explore Workflows

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

Graph Name Retrieved From View
workflow graph io-int-default-tool-and-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/io-int-default-tool-and-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph count-lines2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a
workflow graph DESeq2 Multi-factor Analysis

DESeq2 Multi-factor Analysis Runs DeSeq2 multi-factor analysis with manual control over major parameters

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

Path: workflows/deseq-multi-factor.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-pe-dutp-mitochondrial.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph conflict-wf.cwl#collision

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: 75271e2a0887d47cca4077b60dd51ac763c09b63

Packed ID: collision
workflow graph dynresreq-workflow-stepdefault.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/dynresreq-workflow-stepdefault.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph PerformanceSummaryGenome_v0_1_0.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/PerformanceSummaryGenome_v0_1_0.cwl

Branch/Commit ID: c1aeec7b68acdd1eab3f1d1bd75d768e31abd6d2
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: bbe20f54deea92d9c9cd38cb1f23c4423133d3de

Packed ID: main
workflow graph HBA_calibrator.cwl

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

Path: workflows/HBA_calibrator.cwl

Branch/Commit ID: 035f66ec0f260628424c9621aed97f7cbf35e737
workflow graph ValidateTelescopeStructure

Validate telescope structure by drawing components relevant for ray tracing of photons through the instrument.

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

Path: workflows/ValidateTelescopeStructure.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5