Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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wf-variantcall.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: NA12878-chr20/NA12878-platinum-chr20-workflow-arvados/wf-variantcall.cwl Branch/Commit ID: master |
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collate_unique_SSU_headers.cwl
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: 5833078 |
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download_quality_control.cwl
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https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/sra/download_quality_control.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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bam_readcount workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/bam_readcount.cwl Branch/Commit ID: downsample_and_recall |
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varscan somatic workflow
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/varscan.cwl Branch/Commit ID: downsample_and_recall |
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Unaligned to aligned BAM
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https://github.com/tmooney/cancer-genomics-workflow.git
Path: definitions/subworkflows/align.cwl Branch/Commit ID: downsample_and_recall |
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SetEffectiveFocalLength
Calculate effective focal length for the given telescope optics. |
https://github.com/gammasim/workflows.git
Path: workflows/SetEffectiveFocalLength.cwl Branch/Commit ID: main |
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func_ann_and_post_processing-subwf.cwl
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https://github.com/EBI-Metagenomics/pipeline-v5.git
Path: workflows/subworkflows/assembly/func_ann_and_post_processing-subwf.cwl Branch/Commit ID: master |
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LSU-from-tablehits.cwl
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https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git
Path: tools/LSU-from-tablehits.cwl Branch/Commit ID: 43d2fb8 |
