Workflow: super-enhancer.cwl
Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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bambai_pair | File [BAM] | Coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file |
promoter_bp | Integer | Promoter distance |
Promoter distance for gene names assignment |
islands_file | File [xls] | XLS called peaks file |
XLS file to include information about peaks returned by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl |
tss_distance | Integer | TSS distance |
Distance from TSS to exclude, 0 = no TSS exclusion |
annotation_file | File [TSV] | Annotation file |
Tab-separated input annotation file |
stitch_distance | Integer | Stitching distance |
Linking distance for stitching |
chrom_length_file | File [Textual format] | Chromosome length file |
Chromosome length file |
islands_control_file | File (Optional) [xls] | XLS called peaks file (control) |
XLS file to include information about peaks returned by iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl for control |
Steps
ID | Runs | Label | 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 |
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run_rose |
../tools/rose.cwl
(CommandLineTool)
|
Tool runs ROSE to get Super Enhancers regions -b and -c arguments are not supported |
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sort_bed |
../tools/linux-sort.cwl
(CommandLineTool)
|
Tool sorts data from `unsorted_file` by key |
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rename_png |
../tools/rename.cwl
(CommandLineTool)
|
Tool renames `source_file` to `target_filename`. Input `target_filename` should be set as string. If it's a full path, only basename will be used. If BAI file is present, it will be renamed too |
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bed_to_macs |
../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 |
|
assign_genes |
../tools/iaintersect.cwl
(CommandLineTool)
|
Tool assigns each peak obtained from MACS2 to a gene and region (upstream, promoter, exon, intron, intergenic) |
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bed_to_bigbed |
../tools/ucsc-bedtobigbed.cwl
(CommandLineTool)
|
Tool converts bed file to bigBed |
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add_island_names |
../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 |
---|---|---|---|
png_file | File [PNG] | ROSE visualization plot |
Generated by ROSE visualization plot |
bigbed_file | File [TSV] | Gateway Super Enhancer bigBed file |
Gateway Super Enhancer bigBed file |
gene_names_file | File [TSV] | Gateway Super Enhancer results from ROSE with gene names |
Gateway Super Enhancer results from ROSE with assigned gene names |
https://w3id.org/cwl/view/git/cf84038de256c7ca98657ad81734d1aca1dad8c1/workflows/super-enhancer.cwl