Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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ndppp-pipeline.cwl
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https://github.com/tammojan/dpppcwl.git
Path: ndppp-pipeline.cwl Branch/Commit ID: master |
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metaphlan_wfl.cwl
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https://github.com/stevetsa/Metaphlan-ISBCGC.git
Path: metaphlan_wfl.cwl Branch/Commit ID: master |
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metacal-wf.cwl
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https://github.com/EiffL/metacal-pipeline.git
Path: tools/metacal-wf.cwl Branch/Commit ID: master |
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workflow1_11.cwl#UncompressDatatables.cwl
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https://github.com/GeorgeAlehandro/cwl_1_11.git
Path: workflow1_11.cwl Branch/Commit ID: main Packed ID: UncompressDatatables.cwl |
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word-mapping-dir.cwl#align-texts-wf.cwl
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https://github.com/KBNLresearch/ochre.git
Path: ochre/cwl/word-mapping-dir.cwl Branch/Commit ID: master Packed ID: align-texts-wf.cwl |
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ocrevaluation-performance-test-files-wf-pack.cwl#ocrevaluation-performance-wf.cwl
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https://github.com/kbnlresearch/ochre.git
Path: ochre/cwl/ocrevaluation-performance-test-files-wf-pack.cwl Branch/Commit ID: master Packed ID: ocrevaluation-performance-wf.cwl |
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spaceTxConversion.cwl
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https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git
Path: steps/spaceTxConversion.cwl Branch/Commit ID: master |
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exome alignment and somatic variant detection for cle purpose
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/pipelines/somatic_exome_cle.cwl Branch/Commit ID: downsample_and_recall |
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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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capmq.cwl
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https://github.com/wtsi-hgi/arvados-pipelines.git
Path: cwl/workflows/capmq.cwl Branch/Commit ID: master |