Explore Workflows
View already parsed workflows here or click here to add your own
| Graph | Name | Retrieved From | View |
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wf-svcall.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-svcall.cwl Branch/Commit ID: e561c7e77b0c936f83ddce988f8540c77c42f1fb |
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wf-variantcall.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-variantcall.cwl Branch/Commit ID: e561c7e77b0c936f83ddce988f8540c77c42f1fb |
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Detect DoCM variants
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https://github.com/genome/cancer-genomics-workflow.git
Path: docm/germline_workflow.cwl Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b |
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wf-variantcall.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-variantcall.cwl Branch/Commit ID: 120b79b0a64d6e5bec1b00df9fb09d885a2f71a8 |
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wf-alignment.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-alignment.cwl Branch/Commit ID: 120b79b0a64d6e5bec1b00df9fb09d885a2f71a8 |
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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: 018d344b12e9e1b888e21e0819096f9b337d371d |
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wf-svcall.cwl
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https://github.com/bcbio/bcbio_validation_workflows.git
Path: wes-agha-test/wes_chr21_test-workflow-gcp/wf-svcall.cwl Branch/Commit ID: 120b79b0a64d6e5bec1b00df9fb09d885a2f71a8 |
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CRAM_md5sum_checker_wrapper.cwl
This wraps the md5sum tool with a checker workflow that runs both the tool and a tool that performs verification of results |
https://github.com/DataBiosphere/topmed-workflows.git
Path: CRAM-no-header-md5sum/CRAM_md5sum_checker_wrapper.cwl Branch/Commit ID: e063603e80b382084def46f15f4ecb8968354346 |
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stats.cwl
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https://github.com/EBI-Metagenomics/CWL-assembly.git
Path: cwl/stats/stats.cwl Branch/Commit ID: d3e89b909c89aeb3f4c082f810adce2a6dd32bd5 |
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Unaligned to aligned BAM
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https://github.com/genome/cancer-genomics-workflow.git
Path: unaligned_bam_to_bqsr/align.cwl Branch/Commit ID: 6eb7d35ad46207f4ff49e84106b717e17331eb4b |
