Explore Workflows

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

Graph Name Retrieved From View
workflow graph count-lines1-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: d7b1bf353dcc43c707c49a018f2870584821d389
workflow graph RNA-Seq pipeline paired-end

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph scatter-wf3.cwl#main

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf3.cwl

Branch/Commit ID: 26870e38cec81af880cd3e4789ae6cee8fc27020

Packed ID: main
workflow graph joint genotyping for trios or small cohorts

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 2cec4eebeb3461844b9102b89551b8765c7be348

Packed ID: main
workflow graph kallisto_scatter_synapse_paired_end_workflow2.cwl

https://github.com/CRI-iAtlas/iatlas-workflows.git

Path: Kallisto/workflow/kallisto_scatter_synapse_paired_end_workflow2.cwl

Branch/Commit ID: c7fa0fa9ef94c657b664f680462dbc3f5b7a32e8
workflow graph Unaligned bam to sorted, markduped bam

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

Path: definitions/subworkflows/align_sort_markdup.cwl

Branch/Commit ID: 5cb188131f786ed33156e2f0e3dd63ab9c04245d
workflow graph Tumor-Only Detect Variants workflow

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 40097e1ed094c5b42b68f3db2ff2cbe78c182479
workflow graph picard_markduplicates

Mark duplicates

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/picard_markduplicates.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3
workflow graph segmentation.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/segmentation.cwl

Branch/Commit ID: 5b866e480fb557cf53d619a22068c73548e337d5