Explore Workflows

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

Graph Name Retrieved From View
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: c9e7f3de7f6ba38ee663bd3f9649e8d7dbac0c86
workflow graph Immunotherapy Workflow

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

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 7638b3075863ae8172f4adaec82fb2eb8e80d3d5
workflow graph rRNA_selection.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/rRNA_selection.cwl

Branch/Commit ID: 9a72f76a5c8c874278205fcdeb93362a0d8a5152
workflow graph filter-pcr-artifacts.cwl

DNase-seq - map - Filter PCR Artifacts

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

Path: v1.0/map/filter-pcr-artifacts.cwl

Branch/Commit ID: 487af88ef0b971f76ecd1a215639bb47e3ee94e1
workflow graph echo-wf-default.cwl

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

Path: v1.0/v1.0/echo-wf-default.cwl

Branch/Commit ID: 4fe434e969c93c94b690ba72db295d9d52a6f576
workflow graph GATKBaseRecalBQSRWorkflow_4_1_3.cwl

https://github.com/PMCC-BioinformaticsCore/janis-pipelines.git

Path: janis_pipelines/wgs_somatic/cwl/tools/GATKBaseRecalBQSRWorkflow_4_1_3.cwl

Branch/Commit ID: 5ba65e4781f03a74a845b7cd40bbf4c2ae3a9844
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph 02-trim-se.cwl

ATAC-seq 02 trimming - reads: SE

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

Path: v1.0/ATAC-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: 67e8ccd5abddbd9e27f23ceeb95536fecf792d93
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 041a234a935c7af7d3db95353ef80c61c88fc010
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: 104059e07a2964673e21d371763e33c0afeb2d03