CWL Workflow: bam-bedgraph-bigwig.cwl

Workflow: bam-bedgraph-bigwig.cwl

Fetched 2023-01-12 23:24:33 GMT

Verified with cwltool version 3.1.20221201130942

Workflow converts input BAM file into bigWig and bedGraph files

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.

ID	Type	Title	Doc
dutp	Boolean (Optional)	Enable dUTP	Change strand af the mate read, so both reads come from the same strand
scale	Float (Optional)	Genome coverage scaling coefficient	Coefficient to scale the genome coverage by a constant factor
split	Boolean (Optional)	Split reads by 'N' and 'D'	Calculate genome coverage for each part of the splitted by 'N' and 'D' read
strand	String (Optional)	Enable strand specific genome coverage calculation	Calculate genome coverage of intervals from a specific strand
bam_file	File	Input BAM file	Input BAM file, sorted by coordinates
pairchip	Boolean (Optional)	Enable paired-end genome coverage calculation	Enable paired-end genome coverage calculation
fragment_size	Integer (Optional)	Fixed fragment size	Set fixed fragment size for genome coverage calculation
bigwig_filename	String (Optional)	bigWig output filename	Output filename for generated bigWig
bedgraph_filename	String (Optional)	bedGraph output filename	Output filename for generated bedGraph
chrom_length_file	File	Chromosome length file	Tab delimited chromosome length file: <chromName><TAB><chromSize>
mapped_reads_number	Integer (Optional)	Mapped reads number	Parameter to calculate scale as 1000000/mapped_reads_number. Ignored by bedtools-genomecov.cwl in bam_to_bedgraph step if scale is provided

ID	Runs	Doc
sort_bedgraph	../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.
bam_to_bedgraph	../tools/bedtools-genomecov.cwl (CommandLineTool)	Tool calculates genome coverage from input bam/bed/gff/vcf using `bedtools genomecov` Depending on `input_file` extension additional prefix is used: if `*.bam` use `-ibam`, else use `-i`. `scale` and `mapped_reads_number` inputs result in the same parameter `-scale`. If `scale` is not provided, check if `mapped_reads_number` is not null and calculate `-scale` as `1000000/mapped_reads_number`. If both inputs are null, `bedtools genomecov` will use its default scaling value. `default_output_filename` function returns default output filename and is used when `output_filename` is not provided. Default output file extention is `.tab`. If bedGraph should be generated (check flags `inputs.depth`), extension is updated to `.bedGraph`. Default basename of the output file is generated on the base of `input_file` basename.
sorted_bedgraph_to_bigwig	../tools/ucsc-bedgraphtobigwig.cwl (CommandLineTool)	Tool converts bedGraph to bigWig file. `default_output_filename` function returns filename for generated bigWig if `output_filename` is not provided. Default filename is generated on the base of `bedgraph_file` basename with the updated to `*.bigWig` extension.

ID	Type	Label	Doc
bigwig_file	File	bigWig output file	bigWig output file
bedgraph_file	File	bedGraph output file	bedGraph output file

Permalink: https://w3id.org/cwl/view/git/ae2b231562822ed66b8e35e5452ae7f012416b2a/subworkflows/bam-bedgraph-bigwig.cwl