Explore Workflows

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

Graph Name Retrieved From View
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: beab66d649dd3ee82a013322a5e830875e8556ba
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: 457e101e3fb87e7fd792357afce00ed8ccbfbcdb
workflow graph step-valuefrom4-wf.cwl

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

Path: tests/step-valuefrom4-wf.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph WGS QC workflow

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

Path: definitions/subworkflows/qc_wgs.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph rnaseq-pe.cwl

Runs RNA-Seq BioWardrobe basic analysis with pair-end data file.

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

Path: workflows/rnaseq-pe.cwl

Branch/Commit ID: dc4ee45ed2c5c30e9a1a173c9ea4445f27d3788a
workflow graph sum-wf.cwl

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

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

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
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: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf_mouse.cwl

Branch/Commit ID: 25aa4788dd4efb1cc8ed6f609cb7803896e4d28d
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: ddd748516b25256a461ea9277303406fa2759b00
workflow graph Single-Cell Preprocessing Cell Ranger Pipeline

Devel version of Single-Cell Preprocessing Cell Ranger Pipeline ===============================================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081