Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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01-qc-se.cwl
ATAC-seq 01 QC - reads: SE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/01-qc-se.cwl Branch/Commit ID: v1.0 |
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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: CWLProvTesting |
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repliseq-parta.cwl
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https://github.com/4dn-dcic/pipelines-cwl.git
Path: cwl_awsem_v1/repliseq/repliseq-parta.cwl Branch/Commit ID: dev2 |
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sc_atac_seq_prep_process_init.cwl
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https://github.com/hubmapconsortium/multiome-rna-atac-pipeline.git
Path: sc-atac-seq-pipeline/steps/sc_atac_seq_prep_process_init.cwl Branch/Commit ID: ec8a7e8 |
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ValidateCameraGeometry
Validate camera shape, orientation, and pixel positions |
https://github.com/gammasim/workflows.git
Path: workflows/ValidateCameraGeometry.cwl Branch/Commit ID: main |
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03-map-pe-blacklist-removal.cwl
ATAC-seq 03 mapping - reads: PE |
https://github.com/alexbarrera/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl Branch/Commit ID: v1.0 |
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GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl
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https://github.com/h3abionet/h3agatk.git
Path: workflows/GATK/GATK-Sub-Workflow-h3abionet-indel-no-vqsr.cwl Branch/Commit ID: 1.0.1 |
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workflow.cwl
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https://github.com/aniewielska/rd_pipeline.git
Path: workflow.cwl Branch/Commit ID: master |
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LSU-from-tablehits.cwl
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https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git
Path: tools/LSU-from-tablehits.cwl Branch/Commit ID: c211071 |
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bams2gvcf.woBQSR_male_chrXY_wXTR.cwl
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https://github.com/ddbj/human-reseq.git
Path: Workflows/bams2gvcf.woBQSR_male_chrXY_wXTR.cwl Branch/Commit ID: master |
