Explore Workflows
View already parsed workflows here or click here to add your own
Graph | Name | Retrieved From | View |
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pindel parallel workflow
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![]() Path: definitions/subworkflows/pindel.cwl Branch/Commit ID: low-vaf |
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collapsed_fastq_to_bam.cwl
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![]() Path: workflows/marianas/collapsed_fastq_to_bam.cwl Branch/Commit ID: master |
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Create Genomic Collection for Bacterial Pipeline
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![]() Path: genomic_source/wf_genomic_source.cwl Branch/Commit ID: master |
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dfast-filelist.cwl
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![]() Path: cwl/workflow/dfast-filelist.cwl Branch/Commit ID: master |
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main-somatic-giab-mix.cwl
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![]() Path: somatic-giab-mix/somatic-giab-mix-workflow/main-somatic-giab-mix.cwl Branch/Commit ID: master |
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umi molecular alignment workflow
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![]() Path: definitions/subworkflows/molecular_qc.cwl Branch/Commit ID: downsample_and_recall |
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TOPMed_RNA-seq
TOPMed RNA-seq CWL workflow. Documentation on the workflow can be found [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/README.md). Example input files: [Dockstore.json](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/Dockstore.json) and [rnaseq_pipeline_fastq-example.yml](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/blob/master/workflow/input-examples/rnaseq_pipeline_fastq-example.yml). Quickstart instructions are [here](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL/README.md#Quick Start). [GitHub Repo](https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL) 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: workflow/rnaseq_pipeline_fastq.cwl Branch/Commit ID: master |
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nmrpipe_workflow.cwl
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![]() Path: nmrpipe_workflow.cwl Branch/Commit ID: master |
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chemprodev.cwl
Workflow for the synthesis and purification of 5-methoxytryptamine, based on a series of chemical reactions, extractions, filtrations, and other unit operations. |
![]() Path: chemprodev.cwl Branch/Commit ID: main |
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chksum_seqval_wf_paired_fq.cwl
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![]() Path: cwls/chksum_seqval_wf_paired_fq.cwl Branch/Commit ID: v0.1.0 |