Workflow: bam-genomecov-bigwig.cwl
Fetched 2023-01-11 22:27:10 GMT
Verified with cwltool version 3.1.20221201130942
creates genome coverage bigWig file from .bam file
- Selected
- |
- Default Values
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- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| input | File | ||
| scale | Float (Optional) | ||
| split | Boolean (Optional) | ||
| bigWig | String (Optional) | ||
| strand | String (Optional) | ||
| pairchip | Boolean (Optional) | ||
| genomeFile | File | ||
| mappedreads | Double (Optional) | ||
| fragmentsize | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
../tools/linux-sort.cwl
(CommandLineTool)
|
Tool is used to run sort command with input data |
|
| bigwig |
../tools/ucsc-bedgraphtobigwig.cwl
(CommandLineTool)
|
Tool is used to convert bedGraph to bigWig file |
|
| genomecov |
../tools/bedtools-genomecov.cwl
(CommandLineTool)
|
Tool is used to calculate statistics on the base of FASTQ file quality scores |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| outfile | File | ||
| bed_file | File |
Permalink:
https://w3id.org/cwl/view/git/b1c723fe94cda2d19efc7f792970a31413640d59/workflows/bam-genomecov-bigwig.cwl
