Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
|---|---|---|---|
|
|
gk-parse-current.cwl
|
Path: cwl/gk-parse-current.cwl Branch/Commit ID: master |
|
|
|
collate_unique_rRNA_headers.cwl
|
Path: tools/collate_unique_rRNA_headers.cwl Branch/Commit ID: e1b0fce |
|
|
|
tRNA_selection.cwl
|
Path: tools/tRNA_selection.cwl Branch/Commit ID: 5e82174 |
|
|
|
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) |
Path: topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl Branch/Commit ID: cwlprov_testing |
|
|
|
pipeline-pe-blacklist-removal.cwl
ATAC-seq pipeline - reads: PE - with blacklist removal |
Path: v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl Branch/Commit ID: master |
|
|
|
EMG pipeline v4.0 (paired end version)
|
Path: workflows/emg-pipeline-v4-paired.cwl Branch/Commit ID: master |
|
|
|
Transcripts annotation workflow
|
Path: workflows/TranscriptsAnnotation-i5only-wf.cwl Branch/Commit ID: master |
|
|
|
preprocess_vcf.cwl
This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow. |
Path: preprocess_vcf.cwl Branch/Commit ID: master |
|
|
|
BD Rhapsody™ WTA Analysis Pipeline
The BD Rhapsody™ WTA Analysis Pipeline is used to create sequencing libraries from single cell transcriptomes without having to specify a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file and a transcriptome annotation file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file. |
Path: wf.cwl Branch/Commit ID: main Packed ID: main |
|
|
|
zip_and_index_vcf.cwl
This is a very simple workflow of two steps. It will zip an input VCF file and then index it. The zipped file and the index file will be in the workflow output. |
Path: zip_and_index_vcf.cwl Branch/Commit ID: 1.0.0 |
