CWL Workflow: heatmap.cwl

Workflow: heatmap.cwl

Fetched 2023-01-09 14:13:06 GMT

Verified with cwltool version 3.1.20221201130942

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

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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
threads	Integer (Optional)	Number of threads	Number of threads for those steps that support multithreading
bam_file	File[] [BAM]	BAM files	Array of input BAM files
hist_width	Integer (Optional)	Histogram/Heatmap width, bp	Histogram/Heatmap width, bp
total_reads	Integer[]	Total reads numbers	Array of total reads number for downstream normalization
fragment_size	Integer[]	Fragment sizes	Array of fragment sizes
genelist_file	File [TSV]	Genelist file	Genelist file
hist_bin_size	Integer (Optional)	Histogram/Heatmap bin size, bp	Histogram/Heatmap bin size, bp
export_heatmap	Boolean (Optional)	Export heatmap instead of a histogram	Export heatmap instead of a histogram

Steps

ID	Runs	Doc
make_tag_folders	../tools/heatmap-prepare.cwl (Workflow)	Workflow runs homer-make-tag-directory.cwl tool using scatter for the following inputs - bam_file - fragment_size - total_reads `dotproduct` is used as a `scatterMethod`, so one element will be taken from each array to construct each job: 1) bam_file[0] fragment_size[0] total_reads[0] 2) bam_file[1] fragment_size[1] total_reads[1] ... N) bam_file[N] fragment_size[N] total_reads[N] `bam_file`, `fragment_size` and `total_reads` arrays should have the identical order.
make_tss_heatmap	../tools/homer-annotate-peaks-hist.cwl (CommandLineTool)	Tool is used to produce histogram or heatmaps only. Rest of the functionality is not implemented intentionally. If TSS analysis needed, input peak_file should be centered on TSS, where the 'center' of the peak in the actual TSS. For example: 1 chr4 978796 978796 - 2 chr4 1052109 1052109 + 3 chr4 1105422 1105422 - Skipped arguments: Related to peaks annotation: -organism -gtf -gff -gff3 -gid -ann -mask -p -pdist -pcount -vcf -editDistance -individuals -gene -go -genomeOntology -ratio -rlog -vst -CpG -nfr -nfrSize -gwasCatalog -map -noann Related to tss/tts/rna modes: tss tts rna -list -cTSS Related to motifs: -m -mscore -nmotifs -mdist -mfasta -fm -rmrevopp -matrix -mbed -mlogic -norevopp Related to peak centering: -center -mirror -multi Related to genome comparisons -cmpGenome -cmpLiftover Currently not needed functionality: -bedGraph -wig -nuc -di -histNorm -rm -log -sqrt -len -pc -noblanks -homer1 -homer2
center_genelist_on_tss	../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
heatmap_file_raw	File

Permalink: https://w3id.org/cwl/view/git/1d45ce42181dfce7aceec8bc99a3730eb5285948/workflows/heatmap.cwl