CWL Workflow: Genomic regions intersection and visualization

Workflow: Genomic regions intersection and visualization

Fetched 2023-01-04 16:11:06 GMT

Verified with cwltool version 3.1.20221201130942

Genomic regions intersection and visualization ============================================== 1. Merges intervals within each of the filtered peaks files from ChIP/ATAC experiments 2. Overlaps merged intervals and assigns the nearest genes to them

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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
promoter_dist	Integer (Optional)	Max distance from gene TSS (in both direction) to assign interval to promoter	Max distance from gene TSS (in both direction) overlapping which the interval will be assigned to the promoter region
upstream_dist	Integer (Optional)	Max distance from promoter (only in upstream direction) to assign interval to upstream	Max distance from the promoter (only in upstream direction) overlapping which the interval will be assigned to the upstream region
annotation_file	File [TSV]	Genome to use for the nearest gene assignment	Tab-separated annotation file
intervals_files	File[] [BED]	Filtered ChIP/ATAC experiment	Filtered peaks file from ChIP/ATAC experiment formatted as headerless BED [chrom start end name] file
intervals_aliases	String[]	Filtered ChIP/ATAC experiment	Filtered ChIP/ATAC experiment alias

Steps

ID	Runs	Doc
sort_intervals	intervene.cwl#sort_intervals/3f17f58a-7bdf-4325-a275-d29ff2846fd5 (Workflow)
merge_intervals	intervene.cwl#merge_intervals/11f8d445-c573-490d-a65f-a831d6d236b4 (Workflow)
overlap_intervals	../tools/intervene.cwl (CommandLineTool)	Intervene: a tool for intersection and visualization of multiple genomic regions ================================================================================ Hardcoded parameters: --type genomic use genomic regions as inputs --save-overlaps save overlapping regions/names for all the combinations as bed/txt --project intervene for the guatanteed access to results location -o results for the guatanteed access to results location Skipped parameters: --filenames as it seems not logical to have it when default for --names already uses file names When run in \"pairwise\" mode: --save-overlaps and --overlap-thresh set to null --htype and --diagonal added When run in \"venn\" mode: --colors aren't ignored
remove_empty_columns	../tools/custom-bash.cwl (CommandLineTool)	Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename
get_overlapped_between_all	../tools/get-file-by-name.cwl (ExpressionTool)	Returns file the first file from input File[], that match input regex expression
annotate_overlapped_intervals	intervene.cwl#annotate_overlapped_intervals/87a176e1-7558-47b7-983b-84b003125305 (Workflow)
refactore_overlapped_intervals	intervene.cwl#refactore_overlapped_intervals/597a5180-a38a-4188-83bf-8d331ef339f8 (Workflow)
annotate_overlapped_between_all	../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.
refactore_overlapped_between_all	../tools/custom-bash.cwl (CommandLineTool)	Tool to run custom script set as `script` input with arguments from `param`. Default script runs sed command over the input file and exports results to the file with the same name as input's basename

Outputs

ID	Type	Label	Doc
overlapped_plot	File [PNG]	Intervals overlap diagram	Intervals overlap diagram
intervene_stderr_log	File [Textual format]	intervene stderr log	intervene stderr log
intervene_stdout_log	File [Textual format]	intervene stdout log	intervene stdout log
overlapped_combinations	File (Optional) [Textual format]	Overlapped combinations file	Overlapped combinations file
overlapped_between_all_bed	File [BED]	BED file with common for all inputs intervals	BED file with common for all inputs intervals
overlapped_intervals_files	File[] [TSV]	Overlapped intervals files with the nearest genes assigned	Overlapped intervals files with the nearest genes assigned
annotated_overlapped_between_all_file	File [TSV]	Annotated intervals common for all intersected files	Annotated intervals common for all intersected files

Permalink: https://w3id.org/cwl/view/git/60854b5d299df91e135e05d02f4be61f6a310fbc/workflows/intervene.cwl