Explore Workflows

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

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

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

Path: tests/scatter-valuefrom-wf2.cwl

Branch/Commit ID: 31ec48a8d81ef7c1b2c5e9c0a19e7623efe4a1e2
workflow graph idr.cwl

https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-Seq/idr.cwl

Branch/Commit ID: 7364aa3799fd3bd7584049228618301bda53a3af
workflow graph bulk scRNA-seq pipeline using Salmon

https://github.com/hubmapconsortium/salmon-rnaseq.git

Path: bulk-pipeline.cwl

Branch/Commit ID: 2331bffee5dcedf692ee5a2c0fa9df670d8d7834
workflow graph Trim Galore SMARTer RNA-Seq pipeline paired-end strand specific

https://chipster.csc.fi/manual/library-type-summary.html Modified original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe-smarter-dutp.cwl

Branch/Commit ID: a8eaf61c809d76f55780b14f2febeb363cf6373f
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: e4d6182d5f7a6a880e5f2b21273cf40d25e187df
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684
workflow graph scatter GATK HaplotypeCaller over intervals

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 2f65fc96207a71b1cda4e246f808bed056608cd0
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: 0e98de8f692bb7b9626ed44af835051750ac20cd
workflow graph mut3.cwl

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

Path: tests/wf/mut3.cwl

Branch/Commit ID: a70a83fe14a100cd16e2402ec17b2904f5eeb17d
workflow graph maf2vcf_gz_workflow.cwl

Workflow to convert a maf file into a vcf.gz with .tbi index

https://github.com/mskcc/pluto-cwl.git

Path: cwl/maf2vcf_gz_workflow.cwl

Branch/Commit ID: 342e6f1f4f7a3839e579fbe96ccc8d6f7a61ac77