Workflow: chipseq_tf_align.cwl
Fetched 2023-01-11 21:51:42 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| reads |
Reads to align |
||
| idxbase | File |
Base filename of bwa index to map against |
|
| blacklist | File |
Blacklist regions to remove |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| sort |
tools/samtools-sort.cwl
(CommandLineTool)
|
||
| align |
tools/bwa-mem.cwl
(CommandLineTool)
|
||
| to_bam |
tools/samtools-samtobam.cwl
(CommandLineTool)
|
||
| mark_duplicates |
tools/picard-MarkDuplicates.cwl
(CommandLineTool)
|
||
| remove_unmapped |
tools/samtools-view.cwl
(CommandLineTool)
|
||
| remove_blacklist |
tools/bedtools-intersect.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| processed_reads | File |
Permalink:
https://w3id.org/cwl/view/git/f6346c109000c92ae53183df844eece0ad63eeb7/chipseq_tf_align.cwl
