Explore Workflows

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

Graph Name Retrieved From View
workflow graph bqsr-flow.cwl

Run BQSR pre+post+plot flow

 https://github.com/Sentieon/Sentieon-cwl.git

Path: stage/bqsr-flow.cwl

Branch/Commit ID: 845f4699c5fce96a4c708a553b3701c9cf296653
workflow graph workflow.cwl

https://github.com/AlexanderSenf/pipelines_intro.git

Path: cwl/workflow.cwl

Branch/Commit ID: 4b68929a4f4a0007bec513caa3684c36aeb52322
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph Motif Finding with HOMER with target and background regions from peaks

Motif Finding with HOMER with target and background regions from peaks --------------------------------------------------- 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-peak.cwl

Branch/Commit ID: 4360fb2e778ecee42e5f78f83b78c65ab3a2b1df
workflow graph kmer_seq_entry_extract_wnode

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

Path: task_types/tt_kmer_seq_entry_extract_wnode.cwl

Branch/Commit ID: bb2f26dfe630179737ec2ff08a8614f1f47abcaf
workflow graph Unaligned BAM to BQSR

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

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 389f6edccab082d947bee9c032f59dbdf9f7c325
workflow graph Unaligned BAM to BQSR and VCF

https://github.com/fgomez02/analysis-workflows.git

Path: definitions/subworkflows/bam_to_bqsr.cwl

Branch/Commit ID: 9c9e6a6a48eb321804ce772a2c2c12b4f2f32529
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 5c4125344b1b9125ad04d7e768ecc99901570a7a
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 4f4448f71645275db5b84eb551990dfe3bf37cbb
workflow graph pipeline-se-blacklist-removal.cwl

ATAC-seq pipeline - reads: SE - with blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl

Branch/Commit ID: 8d02684ae0ff27e641f3704686e3bc8b1979b854