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: 5e7385b8cfa4ddae822fff37b6bd22eb0370b389
workflow graph scatter-wf2.cwl

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

Path: cwltool/schemas/v1.0/v1.0/scatter-wf2.cwl

Branch/Commit ID: e8b3565a008d95859fc44227987a54e6a53a8c29
workflow graph sec-wf-out.cwl

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: 047e69bb169e79fad6a7285ee798c4ecec3b218b
workflow graph gatk-4.0.0.0-library-cram-to-gvcfs.cwl

https://github.com/wtsi-hgi/arvados-pipelines.git

Path: cwl/workflows/gatk-4.0.0.0-library-cram-to-gvcfs.cwl

Branch/Commit ID: 95babe5d8779c036e3499940544c7709600929d1
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: c50b80e9b0eaaf4613f9feca44b3463bbfd288d5
workflow graph THOR - differential peak calling of ChIP-seq signals with replicates

What is THOR? -------------- THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework. For more information please refer to: ------------------------------------- Allhoff, M., Sere K., Freitas, J., Zenke, M., Costa, I.G. (2016), Differential Peak Calling of ChIP-seq Signals with Replicates with THOR, Nucleic Acids Research, epub gkw680.

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

Path: workflows/rgt-thor.cwl

Branch/Commit ID: ddc35c559d1ac6aab4972fe1a2b63300c4373f54
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/alignment_wgs.cwl

Branch/Commit ID: cc3e7f1ccfdc7101c22bf88792608504eea7d53a
workflow graph exome alignment and somatic variant detection for cle purpose

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

Path: definitions/pipelines/somatic_exome_cle.cwl

Branch/Commit ID: 9143dc4ebacb9e1df36a712b0be6fa5d982b0c4f