Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-valuefrom-wf5.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf5.cwl

Branch/Commit ID: 7ec307b01442936fad9b1149f4500496557505ff
workflow graph Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

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

Path: definitions/subworkflows/pvacseq.cwl

Branch/Commit ID: f42c889734c8f709ad2fd9090493bcaac8326c98
workflow graph Detect DoCM variants

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

Path: definitions/subworkflows/docm_germline.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph allele-vcf-rnaseq-pe.cwl

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

Path: workflows/allele-vcf-rnaseq-pe.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph Trim Galore RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. Use 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/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: cwltool/schemas/v1.0/v1.0/revsort.cwl

Branch/Commit ID: 09323506da219ba3ddb5313bd83022b52cac9adc
workflow graph io-union-input-default-wf.cwl

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

Path: tests/io-union-input-default-wf.cwl

Branch/Commit ID: 50251ef931d108c09bed2d330d3d4fe9c562b1c3
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: a3e26136043c03192c38c335316d2d36e3e67478
workflow graph io-int-default-wf.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

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

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome_no_verify_bam.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0