Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	schemadef-wf.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/schemadef-wf.cwl Branch/Commit ID: 4d06b9efd26c5813c13684ebcc95547bb75ddfcc
	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)	https://github.com/heliumdatacommons/TOPMed_RNAseq_CWL.git Path: workflow/rnaseq_pipeline_fastq.cwl Branch/Commit ID: 06c6ff20f4e719d7f7224c17b22dce8617e92447
	EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: workflows/emg-qc-paired.cwl Branch/Commit ID: 43d2fb8a5430dc56b55e84e3986d0079cad8d185
	count-lines9-wf.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/count-lines9-wf.cwl Branch/Commit ID: ca8e6661b5cab1f017e5bc4024650722dae4d50b
	EMG assembly for paired end Illumina	https://github.com/farahzkhan/ebi-metagenomics-cwl.git Path: workflows/emg-assembly.cwl Branch/Commit ID: bcfe5f9affd23d52467f69b4b21d1098f0ca95d7
	unix_align_workflow.cwl	https://github.com/NCI-GDC/gdc-dnaseq-cwl.git Path: tools/unix/unix_align_workflow.cwl Branch/Commit ID: 3cb464a3a5c39cc060cd23d9c60918bc9ffb169b
	scatter-valuefrom-wf5.cwl	https://github.com/common-workflow-language/common-workflow-language.git Path: v1.0/v1.0/scatter-valuefrom-wf5.cwl Branch/Commit ID: 8ca5379806ce7db6e47c90d767549bbf7bbcc88f
	SSU-from-tablehits.cwl	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 56dafa4dab5892c5afa35713563dddc78ec5a00d
	collate_unique_SSU_headers.cwl	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: 0cf06f13527b380d21d0f335aaea3e564094ed8f
	functional analysis prediction with InterProScan	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: workflows/functional_analysis.cwl Branch/Commit ID: 3f85843d4a6debdabe96bc800bf2a4efdcda1ef3