Workflow: bed_to_coverage_track.cwl
Fetched 2023-01-14 21:01:13 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 |
|---|---|---|---|
| bed | File | ||
| bin_size | Integer | ||
| genome_info | File | ||
| effective_genome_size | Long | ||
| ignoreForNormalization | String (Optional) |
List of space-delimited chromosome names that shall be ignored when calculating the scaling factor. Specify as space-delimited string. Default: \"chrX chrY chrM\" |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sorting_bam |
../tools/samtools_sort.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
|
| indexing_bam |
../tools/samtools_index_hack.cwl
(CommandLineTool)
|
||
| converting_bed_to_bam |
../tools/bedtools_bedtobam.cwl
(CommandLineTool)
|
||
| converting_bam_to_bigwig |
../tools/deeptools_bamCoverage.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| bigwig | File |
Permalink:
https://w3id.org/cwl/view/git/da07ef9c506ba921438df0bc9f6e1ee57b7d5910/CWL/workflow_modules/bed_to_coverage_track.cwl
