Explore Workflows

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Graph Name Retrieved From View
workflow graph ValidateOpticalPSF

Validate telescope (whole dish) optical point-spread function

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

Path: workflows/ValidateOpticalPSF.cwl

Branch/Commit ID: 789752af87eb190387ff2acb4c95c7a5cdb961e7
workflow graph Workflow that executes the SBG L1 Workflow

https://github.com/unity-sds/sbg-workflows.git

Path: L1-to-L2-e2e.cwl

Branch/Commit ID: 381468e369a8de65fdf33181c04708085fb2c173
workflow graph env-wf2.cwl

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

Path: tests/env-wf2.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph predictions.cwl

https://github.com/simleo/workflow-run-crate.git

Path: docs/examples/draft/ml-predict-pipeline-streamflow/predictions.cwl

Branch/Commit ID: 6382b1aed8804d3d7e041f4800f72e053f9c7a41
workflow graph cond-wf-011.cwl

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

Path: tests/conditionals/cond-wf-011.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903
workflow graph BuildCembaReferences.cwl

https://github.com/common-workflow-lab/wdl-cwl-translator.git

Path: wdl2cwl/tests/cwl_files/BuildCembaReferences.cwl

Branch/Commit ID: 3df778190c16ee0c284a7017ca3173276cb91045
workflow graph dynresreq-workflow-inputdefault.cwl

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

Path: tests/dynresreq-workflow-inputdefault.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph RNA-Seq pipeline paired-end stranded mitochondrial

Slightly changed original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific pair-end** experiment. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with the pair-end strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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/rnaseq-pe-dutp-mitochondrial.cwl

Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph kmer_build_tree

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b