Explore Workflows

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Graph Name Retrieved From View
workflow graph taxcheck.cwl

Perform taxonomic identification tasks on an input genome

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

Path: taxcheck.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph vecscreen.cwl

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

Path: vecscreen/vecscreen.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph iwdr_with_nested_dirs.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph bacterial_screening.cwl

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

Path: vecscreen/bacterial_screening.cwl

Branch/Commit ID: 96dbb414d287f4382e2d477fb1851aeaa5f14f2b
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 2d851682ba1bf2aaaacb3677253b55ceb59c8568
workflow graph Single-Cell RNA-Seq Differential Expression Analysis

Single-Cell RNA-Seq Differential Expression Analysis Identifies differentially expressed genes between any two groups of cells, optionally aggregating gene expression data from single-cell to pseudobulk form.

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

Path: workflows/sc-rna-de-pseudobulk.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph Deprecated. Single-Cell Preprocessing Pipeline

Devel version of Single-Cell Preprocessing Pipeline ===================================================

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

Path: workflows/single-cell-preprocess.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph Generate genome indices for STAR & bowtie

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: dda6e8b5ada3f106a2b3bfcc1b151eccf9977726
workflow graph BD Rhapsody™ Targeted Analysis Pipeline

The BD Rhapsody™ assays are used to create sequencing libraries from single cell transcriptomes. After sequencing, the analysis pipeline takes the FASTQ files and a reference file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.

 https://github.com/longbow0/cwl.git

Path: v1.9-beta/rhapsody_targeted_1.9-beta.cwl

Branch/Commit ID: b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e

Packed ID: main
workflow graph dynresreq-workflow-tooldefault.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/dynresreq-workflow-tooldefault.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94