Explore Workflows

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

Graph Name Retrieved From View
workflow graph kallisto-demo.cwl

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

Path: workflows/kallisto-demo.cwl

Branch/Commit ID: master
workflow graph Trim Galore RNA-Seq pipeline single-read

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.cwl

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

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

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

Branch/Commit ID: main
workflow graph hi-c-processing-pairs-nore-nonorm.cwl

https://github.com/mr-c/4dn-dcic-pipelines-cwl.git

Path: cwl_awsem_v1/hi-c-processing-pairs-nore-nonorm.cwl

Branch/Commit ID: dev2
workflow graph exome alignment and germline variant detection

https://github.com/genome/cancer-genomics-workflow.git

Path: germline_exome_workflow.cwl

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

https://github.com/genome/cancer-genomics-workflow.git

Path: somatic_exome_workflow.cwl

Branch/Commit ID: toil_compatibility
workflow graph workflow-phmmer-blast.cwl

https://github.com/ebi-wp/webservice-cwl.git

Path: workflows/workflow-phmmer-blast.cwl

Branch/Commit ID: master
workflow graph Protein_Inference_workflow_challenge.cwl

https://github.com/adamscharlotte/CWL-workflow.git

Path: Protein_Inference_workflow_challenge.cwl

Branch/Commit ID: master
workflow graph bulk_process.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_process.cwl

Branch/Commit ID: develop
workflow graph count-lines13-wf.cwl

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

Path: tests/count-lines13-wf.cwl

Branch/Commit ID: main