Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf-alignment.cwl

https://github.com/bcbio/test_bcbio_cwl.git

Path: somatic/somatic-workflow/wf-alignment.cwl

Branch/Commit ID: 7ea627c4825d9840cd978a4d17aeb27edc04ae62
workflow graph mirna_profiling.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/mirnaseq/mirna_profiling.cwl

Branch/Commit ID: 3cd06184444bb85e9773a3e7dc548c6dd3bdaccb
workflow graph 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/heliumdatacommons/TOPMed_RNAseq_CWL.git

Path: workflow/rnaseq_pipeline_fastq.cwl

Branch/Commit ID: adc00cfb4abbeab5b975f28780dc50b7c1f555bd
workflow graph wf-variantcall.cwl

https://github.com/bcbio/test_bcbio_cwl.git

Path: somatic/somatic-workflow/wf-variantcall.cwl

Branch/Commit ID: 7ea627c4825d9840cd978a4d17aeb27edc04ae62
workflow graph haplotypecaller.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/haplotypecaller.cwl

Branch/Commit ID: 1595f2bc453663c9e71c1a2d60729f481921029e
workflow graph download_prep.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/download_prep.cwl

Branch/Commit ID: 1595f2bc453663c9e71c1a2d60729f481921029e
workflow graph gatk3_realignment.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/realignment/gatk3_realignment.cwl

Branch/Commit ID: 1595f2bc453663c9e71c1a2d60729f481921029e
workflow graph alignment_bwa_mem.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/harmonization/alignment_bwa_mem.cwl

Branch/Commit ID: 1595f2bc453663c9e71c1a2d60729f481921029e
workflow graph wf_makeblastdb.cwl

https://github.com/ncbi/pipelines.git

Path: amr_finder/wf_makeblastdb.cwl

Branch/Commit ID: 85bd1acfc587e6a3ebce7ccf1ce93bf8b48e881c
workflow graph upload_results.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/utils/upload_results.cwl

Branch/Commit ID: 1595f2bc453663c9e71c1a2d60729f481921029e