Explore Workflows
View already parsed workflows here or click here to add your own
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scatter GATK HaplotypeCaller over intervals
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Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl Branch/Commit ID: master |
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PrediXcan
Predict.py has been wrapped in cwl, getting the information from: https://github.com/hakyimlab/MetaXcan/wiki/Individual-level-PrediXcan:-introduction,-tutorials-and-manual Here is a snippet from: https://github.com/hakyimlab/MetaXcan/wiki/Individual-level-PrediXcan:-introduction,-tutorials-and-manual In the following, we focus on the individual-level implementation of PrediXcan. The method was originally implemented in this repository. PrediXcan consists of two steps: Predict gene expression (or whatever biology the models predict) in a cohort with available genotypes Run associations to a trait measured in the cohort The first step is implemented in Predict.py. The prediction models are trained and pre-compiled on specific data sets with their own human genome releases and variant definitions. We implemented a few rules to support variant matching from genotypes based on different variant definitions. In the following, mapping refers to the process of assigning a model variant to a genotype variant. Originally, PrediXcan was applied to genes so we say \"gene expression\" a lot as it was the mechanism we initially studied. But conceptually, everything said here applies to any intermediate/molecular mechanism such as splicing or brain morphology. Whenever we say \"gene\", it generally could mean a splicing intron event, etc. |
Path: predixcan/predixcan_unpack.cwl Branch/Commit ID: main |
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snpeff-workflow.cwl
Annotate variants provided in a gziped VCF using SnpEff |
Path: snpeff-workflow.cwl Branch/Commit ID: master |
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pcawg_annotate_wf.cwl
This workflow will run OxoG, variantbam, and annotate. Run this as `dockstore --script --debug workflow launch --descriptor cwl --local-entry --entry ./oxog_varbam_annotate_wf.cwl --json oxog_varbam_annotat_wf.input.json ` |
Path: pcawg_annotate_wf.cwl Branch/Commit ID: master |
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Dockstore.cwl
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Path: Dockstore.cwl Branch/Commit ID: master |
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RNASelector as a CWL workflow
https://doi.org/10.1007/s12275-011-1213-z |
Path: workflows/rna-selector.cwl Branch/Commit ID: 5dc7c5c |
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CNV_pipeline
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Path: structuralvariants/cwl/workflow.cwl Branch/Commit ID: master |
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collect_pair_files.cwl
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Path: modules/pair/collect_pair_files.cwl Branch/Commit ID: master |
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exome alignment and germline variant detection
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Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: downsample_and_recall |
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example_workflow.cwl
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Path: example_workflow.cwl Branch/Commit ID: main |
