Explore Workflows
View already parsed workflows here or click here to add your own
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EMG assembly for paired end Illumina
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Path: workflows/emg-assembly.cwl Branch/Commit ID: 3168316 |
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CRAM_md5sum_checker_wrapper.cwl
This wraps the md5sum tool with a checker workflow that runs both the tool and a tool that performs verification of results |
Path: CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl Branch/Commit ID: 1.24.0 |
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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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Dockstore.cwl
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Path: Dockstore.cwl Branch/Commit ID: master |
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WGS processing workflow for single sample
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Path: WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl Branch/Commit ID: main |
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chksum_seqval_wf_paired_fq.cwl
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Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: 0.4.1 |
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scatter-valuefrom-inputs-wf1.cwl
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Path: tests/scatter-valuefrom-inputs-wf1.cwl Branch/Commit ID: master |
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multiome pipeline using Salmon and Alevin (HuBMAP scRNA-seq pipeline) and HuBMAP scATAC-seq pipeline
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Path: pipeline.cwl Branch/Commit ID: a33bc8a |
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Genome conversion and annotation
Workflow for genome annotation from EMBL format |
Path: cwl/workflows/workflow_sapp_others.cwl Branch/Commit ID: master |
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varscan somatic workflow
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Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: No_filters_detect_variants |
