Explore Workflows

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

Graph Name Retrieved From View
workflow graph Task2

For CMRxRecon validation

https://github.com/CmrxRecon/CMRxRecon2024-snippets.git

Path: workflow-task2.cwl

Branch/Commit ID: 5b55ee7ba12f81d938a909d75d8c48e51361b4cf
workflow graph env-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: 6d2998467fada81e5024c1f8594ae167514cb290
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: 564156a9e1cc7c3679a926c479ba3ae133b1bfd4
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 4ae14dd3a447c90022e3dfeb53fc05b8436e2775
workflow graph Generate genome indices for Bismark

Copy genome_fasta file to the folder and run run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the genome_fasta file basename without extension.

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

Path: workflows/bismark-indices.cwl

Branch/Commit ID: c602e3cdd72ff904dd54d46ba2b5146eb1c57022
workflow graph Detect Docm variants

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

Path: definitions/subworkflows/docm_cle.cwl

Branch/Commit ID: 6949082038c1ad36d6e9848b97a2537aef2d3805
workflow graph Single-Cell Preprocessing Cell Ranger Pipeline

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

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

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

Branch/Commit ID: 57437c1e9f881411b65f79acd64b7cf14df5b901
workflow graph Seurat for comparative scRNA-seq analysis of across experimental conditions

Runs Seurat for comparative scRNA-seq analysis of across experimental conditions ================================================================================

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

Path: workflows/seurat-cluster.cwl

Branch/Commit ID: 57437c1e9f881411b65f79acd64b7cf14df5b901
workflow graph scatter-valuefrom-wf1.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/scatter-valuefrom-wf1.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph star_align_workflow.cwl

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

Path: workflows/subworkflows/rnaseq_processing/star_align_workflow.cwl

Branch/Commit ID: f0594206c230e53ad3ad9de14364fc6bce1d5cb7