CWL Workflow: ROSE: rank ordering of super-enhancers

Workflow: ROSE: rank ordering of super-enhancers

Fetched 2023-01-14 19:17:05 GMT

Verified with cwltool version 3.1.20221201130942

Super-enhancers, consist of clusters of enhancers that are densely occupied by the master regulators and Mediator. Super-enhancers differ from typical enhancers in size, transcription factor density and content, ability to activate transcription, and sensitivity to perturbation. Use to create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)

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Default Values
Nested Workflows
Tools
Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
alias	String	Experiment short name/Alias
peak_file	File [xls]	ChIP-Seq experiment	XLS file generated by MACS2
alignment_file	File [BAM]	ChIP-Seq experiment	Coordinate sorted BAM file and BAI index file
annotation_file	File [TSV]	Genome annotation	TSV genome annotation file
chrom_length_file	File [Textual format]	Chromosome length file	Chromosome length file
peak_control_file	File (Optional) [xls]	Control ChIP-Seq experiment	XLS file generated by MACS2 used as control
promoter_distance	Integer (Optional)	Promoter distance, bp	Max distance from gene TSS (in both direction) overlapping which the peak will be assigned to the promoter region. Default: 1000 bp
upstream_distance	Integer (Optional)	Upstream distance, bp	Max distance from the promoter (only in upstream direction) overlapping which the peak will be assigned to the upstream region. Default: 20,000 bp
stitching_distance	Integer (Optional)	Maximum distance between two regions that will be stitched together	Maximum distance between two regions that will be stitched together. For ROSE default is 12.5kb, in workflow default is 20000
tss_exclusion_zone_size	Integer (Optional)	Exclude regions contained within +/- this distance from TSS (skip TSS exclusion if 0)	Exclude regions contained within +/- this distance from TSS in order to account for promoter biases (Default: 0; recommended if used: 2500). If this value is 0, will not look for a gene file

Steps

ID	Runs	Doc
make_gff	../tools/makegff.cwl (CommandLineTool)	Tool produces GFF output from the file generated by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl tool Both islands_file and islands_control_file should be produced by the same tool
run_rose	../tools/rose.cwl (CommandLineTool)	Tool runs ROSE to get Super Enhancers regions -b and -c arguments are not supported
sort_bed	../tools/linux-sort.cwl (CommandLineTool)	Tool sorts data from `unsorted_file` by key `default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.
reduce_bed	super-enhancer.cwl#reduce_bed/64b06fd9-20aa-43da-9e43-58e8a7d060ea (CommandLineTool)	Tool converts BED6 to BED4 by reducing column numbers
rename_png	super-enhancer.cwl#rename_png/ea5246b0-f901-473d-8f5a-3829b5ccd5a3 (CommandLineTool)	Tool renames (copy) `source_file` to `target_filename`
bed_to_macs	super-enhancer.cwl#bed_to_macs/c86b30f0-a40d-4ad0-9269-c8c7284cd898 (CommandLineTool)	Tool converts `input_file` to the format compatible with the input of iaintersect from `assign_genes` step
assign_genes	../tools/iaintersect.cwl (CommandLineTool)	Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic) `default_output_filename` function returns output filename with sufix set as `ext` argument. Function is called when either `output_filename` or `log_filename` inputs are not provided.
bed_to_bigbed	super-enhancer.cwl#bed_to_bigbed/32f9cb4b-909c-4ec6-9f69-97a32778869d (CommandLineTool)	Tool converts bed to bigBed
add_island_names	super-enhancer.cwl#add_island_names/b80830ac-dc8a-46f4-b38c-148a11a3823a (CommandLineTool)

Outputs

ID	Type	Label	Doc
super_enhancers_raw_txt	File [Textual format]	Super-enhancers report file (raw, from ROSE)	Super-enhancers report file (raw, from ROSE)
super_enhancers_bigbed_file	File [bigBed]	Super-enhancers	Super-enhancers bigBed file
super_enhancers_report_file	File [TSV]	Super-enhancers report file with assigned genes	Super-enhancers report file with assigned genes
ranked_super_enhancers_plot_png	File [PNG]	Ranked super-enhancers plot	Ranked super-enhancers plot

Permalink: https://w3id.org/cwl/view/git/104059e07a2964673e21d371763e33c0afeb2d03/workflows/super-enhancer.cwl