Explore Workflows

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

Graph Name Retrieved From View
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph qc-assembled.workflow.cwl

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/qc-assembled.workflow.cwl

Branch/Commit ID: d9cf22cd615542c94f7974e8bce4cf29b24d985f
workflow graph Cell Ranger Count (RNA)

Cell Ranger Count (RNA) Quantifies single-cell gene expression of the sequencing data from a single 10x Genomics library. The results of this workflow are primarily used in either “Single-Cell RNA-Seq Filtering Analysis” or “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines.

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph gp_makeblastdb

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

Path: progs/gp_makeblastdb.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph Single-Cell RNA-Seq Dimensionality Reduction Analysis

Single-Cell RNA-Seq Dimensionality Reduction Analysis Removes noise and confounding sources of variation by reducing dimensionality of gene expression data from the outputs of “Single-Cell RNA-Seq Filtering Analysis” or “Single-Cell Multiome ATAC and RNA-Seq Filtering Analysis” pipelines. The results of this workflow are primarily used in “Single-Cell RNA-Seq Cluster Analysis” or “Single-Cell WNN Cluster Analysis” pipelines.

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

Path: workflows/sc-rna-reduce.cwl

Branch/Commit ID: 30031ca5e69cec603c4733681de54dc7bffa20a3
workflow graph tt_hmmsearch_wnode.cwl

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 54c5074587af001a44eccb4762a4cb25fa24cb3e
workflow graph linc_target.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target.cwl

Branch/Commit ID: 0c5bd78e3f2d08564f5c9a563bcc8bb7704e6202
workflow graph exome alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: c235dc6d623879a6c4f5fb307f545c9806eb2d23
workflow graph search.cwl#main

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/search.cwl

Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c

Packed ID: main