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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: 2caa50434966ebdf4b33e5ca689c2e4df32f9058

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

Path: cwltool/schemas/v1.0/v1.0/count-lines1-wf.cwl

Branch/Commit ID: bfe56f3138e9e6fc0b9b8c06447553d4cea03d59

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: ee30368e4f9175c76e194c9f5fa734a5ca4b767c

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/assembly/cmsearch-multimodel-assembly.cwl

Branch/Commit ID: 4b98d8bf882bc96d924b5d2d4e6d9c188fa7b273

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 6d04f5d65d1d4893706d9ae7e27341633333054f

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

Path: definitions/subworkflows/duplex_alignment.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 814bd0405a7701efc7d63e8f0179df394c7766f7

Packed ID: main

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_calibrator.cwl

Branch/Commit ID: efd84bf3c56117c6a05852b3b47aaf4ad8de11bd

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

Path: cwltool/schemas/v1.0/v1.0/count-lines12-wf.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621

Proteins - predict, filter, cluster, identify, annotate

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/protein-filter-annotation.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a