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Showing results for "rnaseq" (Show all)
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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: master |
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samtoolsW.cwl
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in This is a proposed standard operating procedure for genomic variant detection using VARSCAN. It is hoped to be effective and useful for getting SARS-CoV-2 genome variants. It uses Illumina RNASEQ reads and genome sequence. |
https://github.com/ambarishK/bio-cwl-tools.git
Path: samtoolsW.cwl Branch/Commit ID: release |
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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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NonSpliced RNAseq workflow
Workflow for NonSpliced RNAseq data alignment with multiple aligners. Steps: - workflow_illumina_quality.cwl: - FastQC (control) - fastp (trimming) - bowtie2 (read mapping) - sam_to_sorted-bam - featurecounts (transcript read counts) - kallisto (transcript [pseudo]counts) |
https://git.wur.nl/unlock/cwl.git
Path: cwl/workflows/workflow_RNAseq_NonSpliced.cwl Branch/Commit ID: master |
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TOPMed_RNA-seq
TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/cwl_workflows/blob/master/topmed-workflows/TOPMed_RNAseq_pipeline/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/cwl_workflows) 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/FarahZKhan/cwl_workflows.git
Path: topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl Branch/Commit ID: cwlprov_testing |
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allele-vcf-rnaseq-pe.cwl
Allele specific RNA-Seq (using vcf) paired-end workflow |
https://github.com/datirium/workflows.git
Path: workflows/allele-vcf-rnaseq-pe.cwl Branch/Commit ID: 94471ee6c01b7bc17102e45e56e7366c2a52acdf |
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rnaseq-pe.cwl
RNA-Seq basic analysis workflow for paired-end experiment. |
https://github.com/datirium/workflows.git
Path: workflows/rnaseq-pe.cwl Branch/Commit ID: 94471ee6c01b7bc17102e45e56e7366c2a52acdf |
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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: cf84038de256c7ca98657ad81734d1aca1dad8c1 |
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gdc_rnaseq_main_workflow.cwl
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https://github.com/NCI-GDC/gdc-rnaseq-cwl.git
Path: rnaseq-star-align/subworkflows/gdc_rnaseq_main_workflow.cwl Branch/Commit ID: 88fb720c62a3c2b00ca475d412fba088c4a08f92 |
