Explore Workflows

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Graph Name Retrieved From View
workflow graph 03-map-pe-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: PE - blacklist removal

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph ChIP-seq peak caller workflow MACS2 based

This workflow execute peak caller and QC for ChIP-seq using MACS2

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/ChIP-Seq/peak-calling-MACS2.cwl

Branch/Commit ID: 0207b0171ab142dfb85db9c39050c5b4be51dd9e
workflow graph haplotypecaller.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/haplotypecaller.cwl

Branch/Commit ID: c661469505c606e1353f23c21a6654724a9d8d63
workflow graph Motif Finding with HOMER with custom background regions

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 799575ce58746813f066a665adeacdda252d8cab
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 6ac47e5703d8c8cdac698de91143829b3911e9b2
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_germline.cwl

Branch/Commit ID: 3a287b7cb6162cdea79865235d224fea45963d87
workflow graph Build Bismark indices

Copy fasta_file 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 input.

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

Path: workflows/bismark-index.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph 01-qc-pe.cwl

ATAC-seq 01 QC - reads: PE

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

Path: v1.0/ATAC-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: 8aabde14169421a7115c5cd48c4740b3a7bd818f
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 1b9094d70f620bb2e51072dd2150150aa4927439
workflow graph umi molecular alignment fastq workflow

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

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5