Explore Workflows

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: 57437c1e9f881411b65f79acd64b7cf14df5b901

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines9-wf-noET.cwl

Branch/Commit ID: 707ebcd2173889604459c5f4ffb55173c508abb3

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

Path: testdata/step_valuefrom5_wf_with_id_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/workflow_input_format_expr_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/count-lines7-single-source-wf_v1_2.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/workflow_input_format_expr_v1_1.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: testdata/step-valuefrom3-wf_v1_1.cwl

Branch/Commit ID: 15c8467d6d3c31a95ccc682095cf34aad125ca8c

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 24e5290aec441665c6976ee3ee8ae3574c49c6b5

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

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

Path: workflows/heatmap.cwl

Branch/Commit ID: 9a2c389364674221fab3f0f6afdda799e6aa3247

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

https://github.com/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: dc4ee45ed2c5c30e9a1a173c9ea4445f27d3788a