Explore Workflows
View already parsed workflows here or click here to add your own
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EMG pipeline v3.0 (single end version)
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![]() Path: workflows/emg-pipeline-v3.cwl Branch/Commit ID: 3f85843 |
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1st-workflow.cwl
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![]() Path: 1st-workflow.cwl Branch/Commit ID: main |
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SSU-from-tablehits.cwl
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![]() Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: d4e5e53 |
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binning.cwl
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![]() Path: workflows/binning.cwl Branch/Commit ID: master |
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TransDecoder 2 step workflow, running TransDecoder.LongOrfs (step 1) followed by TransDecoder.Predict (step2)
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![]() Path: workflows/TransDecoder-v5-wf-2steps.cwl Branch/Commit ID: assembly |
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fastqc-0-11-4-1.cwl
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![]() Path: cwl_awsem_v1/fastqc-0-11-4-1.cwl Branch/Commit ID: dev2 |
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hi-c-processing-pairs-nore.cwl
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![]() Path: cwl_awsem_v1/hi-c-processing-pairs-nore.cwl Branch/Commit ID: master |
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wf-variantcall.cwl
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![]() Path: wes-agha-test/wes_chr21_test-workflow-arvados/wf-variantcall.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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Create target and anti-target files for CNA analysis
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![]() Path: subworkflows/cnvkit_prep_regions.cwl Branch/Commit ID: master |