Workflow: bam-bedgraph-bigwig.cwl

Fetched 2020-06-03 13:04:27 GMT
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Inputs

ID Type Title Doc
dutp Boolean (Optional) Enable dUTP

Change strand af the mate read, so both reads come from the same strand

bedgraph_filename String (Optional) bedGraph output filename

Output filename for generated bedGraph

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

bigwig_filename String (Optional) bigWig output filename

Output filename for generated bigWig

chrom_length_file File Chromosome length file

Tab delimited chromosome length file: <chromName><TAB><chromSize>

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

scale Float (Optional) Genome coverage scaling coefficient

Coefficient to scale the genome coverage by a constant factor

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

fragment_size Integer (Optional) Fixed fragment size

Set fixed fragment size for genome coverage calculation

Steps

ID Runs Label Doc
sorted_bedgraph_to_bigwig
../tools/ucsc-bedgraphtobigwig.cwl (CommandLineTool)
sort_bedgraph
../tools/linux-sort.cwl (CommandLineTool)
bam_to_bedgraph
../tools/bedtools-genomecov.cwl (CommandLineTool)

Outputs

ID Type Label Doc
bedgraph_file File bedGraph output file

bedGraph output file

bigwig_file File bigWig output file

bigWig output file

Permalink: https://w3id.org/cwl/view/git/f28d47bd0911e5e7210c4dc83f75653a1e0297c9/subworkflows/bam-bedgraph-bigwig.cwl