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workflow graph 05-quantification.cwl

ATAC-seq - Quantification

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

Path: v1.0/ATAC-seq_pipeline/05-quantification.cwl

Branch/Commit ID: 8aabde14169421a7115c5cd48c4740b3a7bd818f
workflow graph main-NA24385-sv.cwl

https://github.com/bcbio/bcbio_validation_workflows.git

Path: NA24385-sv/NA24385-sv-workflow/main-NA24385-sv.cwl

Branch/Commit ID: af9a5621efcb44c249697d6df071fe4defe389ac
workflow graph Motif Finding with HOMER with random background regions

Motif Finding with HOMER with random 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. Here is how we generate background for Motifs Analysis ------------------------------------- 1. Take input file with regions in a form of “chr\" “start\" “end\" 2. Sort and remove duplicates from this regions file 3. Extend each region in 20Kb into both directions 4. Merge all overlapped extended regions 5. Subtract not extended regions from the extended ones 6. Randomly distribute not extended regions within the regions that we got as a result of the previous step 7. Get fasta file from these randomly distributed regions (from the previous step). Use it as background 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.cwl

Branch/Commit ID: 799575ce58746813f066a665adeacdda252d8cab
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph strelkaSomaticVariantCaller_v0_1_1.cwl

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

Path: janis_pipelines/wgs_somatic/cwl/tools/strelkaSomaticVariantCaller_v0_1_1.cwl

Branch/Commit ID: 5ba65e4781f03a74a845b7cd40bbf4c2ae3a9844
workflow graph align_sort_sa

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

Path: task_types/tt_align_sort_sa.cwl

Branch/Commit ID: 75ea689c0a8c9902b4598b453455857cb08e885a
workflow graph bulk_process.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_process.cwl

Branch/Commit ID: e1af1eb62aa9f757bded9b995411d25e098b3572
workflow graph format_rrnas_from_seq_entry

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: a402541b8530f30eab726c160da90a23036847a1
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: 04d21c33a5f2950e86db285fa0a32a6659198d8a
workflow graph nestedworkflows.cwl

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

Path: _includes/cwl/22-nested-workflows/nestedworkflows.cwl

Branch/Commit ID: fb086088825d19c1136b97dd5997a060da8d44d6