Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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pulsar_timing_prototype_workflow.cwl
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https://github.com/TMCantwell/pulsar_timing_prototype.git
Path: pulsar_timing_prototype_workflow.cwl Branch/Commit ID: master |
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Bisulfite alignment and QC
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https://github.com/fgomez02/analysis-workflows.git
Path: definitions/pipelines/bisulfite.cwl Branch/Commit ID: No_filters_detect_variants |
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EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: workflows/emg-qc-single.cwl Branch/Commit ID: master |
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EMG assembly for paired end Illumina
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/emg-assembly.cwl Branch/Commit ID: master |
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RNASelector as a CWL workflow
https://doi.org/10.1007/s12275-011-1213-z |
https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/rna-selector.cwl Branch/Commit ID: master |
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EMG core analysis
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: workflows/emg-core-analysis-v4.cwl Branch/Commit ID: master |
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BioExcel-CWL-firstWorkflow.cwl
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https://github.com/bioexcel/biobb_wf_cwl_tutorial.git
Path: biobb_wf_cwl_tutorial/examples/BioExcel-CWL-firstWorkflow.cwl Branch/Commit ID: master |
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TOPMed_RNA-seq
TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL) Pipeline steps: 1. Align RNA-seq reads with [STAR v2.5.3a](https://github.com/alexdobin/STAR). 2. Run [Picard](https://github.com/broadinstitute/picard) [MarkDuplicates](https://broadinstitute.github.io/picard/command-line-overview.html#MarkDuplicates). 2a. Create BAM index for MarkDuplicates BAM with [Samtools 1.6](https://github.com/samtools/samtools/releases) index. 3. Transcript quantification with [RSEM 1.3.0](https://deweylab.github.io/RSEM/) 4. Gene quantification and quality control with [RNA-SeQC 1.1.9](https://github.com/francois-a/rnaseqc) |
https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git
Path: workflow/rnaseq_pipeline_fastq.cwl Branch/Commit ID: master |
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snaptools_create_snap_file.cwl
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https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git
Path: steps/snaptools_create_snap_file.cwl Branch/Commit ID: 5465f66 |
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exomeseq-03-organizedirectories.cwl
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https://github.com/Duke-GCB/bespin-cwl.git
Path: subworkflows/exomeseq-03-organizedirectories.cwl Branch/Commit ID: gatk4-fixes |
