Explore Workflows
View already parsed workflows here or click here to add your own
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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) |
![]() Path: topmed-workflows/TOPMed_RNAseq_pipeline/rnaseq_pipeline_fastq.cwl Branch/Commit ID: cwlprov_testing |
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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: develop |
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msi.cwl
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![]() Path: workflows/subworkflows/msi.cwl Branch/Commit ID: master |
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Transcripts annotation workflow
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![]() Path: workflows/TranscriptsAnnotation-wf.cwl Branch/Commit ID: master |
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collect_pair_files.cwl
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![]() Path: modules/pair/collect_pair_files.cwl Branch/Commit ID: master |
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chunking-subwf-hmmsearch.cwl
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![]() Path: workflows/subworkflows/chunking-subwf-hmmsearch.cwl Branch/Commit ID: master |
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collate_unique_SSU_headers.cwl
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![]() Path: tools/collate_unique_SSU_headers.cwl Branch/Commit ID: a8abd0e |
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EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.
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![]() Path: workflows/emg-qc-paired.cwl Branch/Commit ID: f6b5196 |
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exome alignment and germline variant detection
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![]() Path: definitions/pipelines/germline_exome.cwl Branch/Commit ID: low-vaf |
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SSU-from-tablehits.cwl
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![]() Path: tools/SSU-from-tablehits.cwl Branch/Commit ID: 135976d |