Explore Workflows

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

Graph Name Retrieved From View
workflow graph id_to_json_workflow.cwl

https://github.com/sfu-ireceptor/airr-seqaa.git

Path: cwl/id_to_json_workflow.cwl

Branch/Commit ID: master
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: dev
workflow graph dedup-3-pass-distr.cwl

run 3-pass dedup: algo LocusCollector + algo Dedup output_dup_read_name + algo Dedup dedup_by_read_name sequentially in distributed mode

 https://github.com/sentieon/sentieon-cwl.git

Path: stage/dedup-3-pass-distr.cwl

Branch/Commit ID: master
workflow graph host.sort.workflow.cwl

https://github.com/azzaea/cwl-scalability-vis.git

Path: host.sort.workflow.cwl

Branch/Commit ID: main
workflow graph 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: master
workflow graph Unaligned to aligned BAM

https://github.com/MarkRobbo/workflows.git

Path: workflows/hello/exome_alignment_packed.cwl

Branch/Commit ID: master

Packed ID: align.cwl
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/FarahZKhan/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: master
workflow graph trim-rnaseq-pe-dutp.cwl

Runs RNA-Seq BioWardrobe basic analysis with strand specific pair-end data file.

https://github.com/Barski-lab/workflows.git

Path: workflows/trim-rnaseq-pe-dutp.cwl

Branch/Commit ID: master
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: f993cad
workflow graph rRNA_selection.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: fa86fce