Workflow: bam-bedgraph-bigwig.cwl
Fetched 2023-01-05 02:44:56 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- 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 |
|---|---|---|---|
| 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 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort_bedgraph |
../tools/linux-sort.cwl
(CommandLineTool)
|
||
| bam_to_bedgraph |
../tools/bedtools-genomecov.cwl
(CommandLineTool)
|
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| sorted_bedgraph_to_bigwig |
../tools/ucsc-bedgraphtobigwig.cwl
(CommandLineTool)
|
Outputs
| 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/f28d47bd0911e5e7210c4dc83f75653a1e0297c9/subworkflows/bam-bedgraph-bigwig.cwl
