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Graph Name Retrieved From View
workflow graph AltAnalyze Prepare Genome

Devel version of AltAnalyze Prepare Genome ========================================== hg38 is not supported. Use hardcoded EnsMart72 until AltAnalyze starts support more recent Ensembl releases.

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

Path: workflows/altanalyze-prepare-genome.cwl

Branch/Commit ID: 7ced5a5259dbd8b3fc64456beaeffd44f4a24081
workflow graph Chipseq alignment with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
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: 8a92669a566589d80fde9d151054ffc220ed4ddd
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: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
workflow graph bam_readcount workflow

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

Path: definitions/subworkflows/bam_readcount.cwl

Branch/Commit ID: 2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71
workflow graph Cellranger reanalyze - reruns secondary analysis performed on the feature-barcode matrix

Devel version of Single-Cell Cell Ranger Reanalyze ================================================== Workflow calls \"cellranger aggr\" command to rerun secondary analysis performed on the feature-barcode matrix (dimensionality reduction, clustering and visualization) using different parameter settings. As an input we use filtered feature-barcode matrices in HDF5 format from cellranger count or aggr experiments. Note, we don't pass aggregation_metadata from the upstream cellranger aggr step. Need to address this issue when needed.

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

Path: workflows/cellranger-reanalyze.cwl

Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_nonhuman.cwl

Branch/Commit ID: 8c4e7372247a7f4ed9ed478ef8ea1d239bc88af0