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Showing results for "rnaseq" (Show all)
Graph | Name | Retrieved From | View |
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trim-rnaseq-se.cwl
Runs RNA-Seq BioWardrobe basic analysis with single-end data file. |
https://github.com/datirium/workflows.git
Path: workflows/trim-rnaseq-se.cwl Branch/Commit ID: 94471ee6c01b7bc17102e45e56e7366c2a52acdf |
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rnaseq_pipeline_fastq_checker-tar.cwl
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https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git
Path: workflow/checker-workflows/rnaseq_pipeline_fastq_checker-tar.cwl Branch/Commit ID: master |
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Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/pvacseq.cwl Branch/Commit ID: downsample_and_recall |
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allele-vcf-rnaseq-se.cwl
Allele specific RNA-Seq (using vcf) single-read workflow |
https://github.com/datirium/workflows.git
Path: workflows/allele-vcf-rnaseq-se.cwl Branch/Commit ID: e284e3f6dff25037b209895c52f2abd37a1ce1bf |
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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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rnaseq_pipeline_fastq_checker.cwl
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https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git
Path: workflow/checker-workflows/rnaseq_pipeline_fastq_checker.cwl Branch/Commit ID: master |
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rnaseq-pe-dutp-mitochondrial.cwl
RNA-Seq strand specific mitochondrial workflow for pair-end experiment based on BioWardrobe's basic analysis. |
https://github.com/datirium/workflows.git
Path: workflows/rnaseq-pe-dutp-mitochondrial.cwl Branch/Commit ID: 9a2c389364674221fab3f0f6afdda799e6aa3247 |
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rnaseq-se.cwl
Runs RNA-Seq BioWardrobe basic analysis with single-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/rnaseq-se.cwl Branch/Commit ID: dcf683418d101917852b1711a91af817d4ea5d03 |
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trim-rnaseq-pe.cwl
Runs RNA-Seq BioWardrobe basic analysis with pair-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/trim-rnaseq-pe.cwl Branch/Commit ID: dcf683418d101917852b1711a91af817d4ea5d03 |
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rnaseq-pe-dutp.cwl
Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file. |
https://github.com/Barski-lab/workflows.git
Path: workflows/rnaseq-pe-dutp.cwl Branch/Commit ID: dcf683418d101917852b1711a91af817d4ea5d03 |