Workflow: bwameth_singlelib.cwl
Fetched 2024-05-09 01:21:29 GMT
Verified with cwltool version 3.1.20230201224320
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| ref | File | ||
| pbat | Boolean | ||
| read1 | File[] | ||
| read2 | File[] | ||
| threads | Integer | ||
| output_name | String | ||
| illuminaclip | String | ||
| adapters_file | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| trim |
../../tools/trimming/trimmomatic.cwl
(CommandLineTool)
|
||
| qc_pretrim |
../../tools/fastqc.cwl
(CommandLineTool)
|
||
| methydackel |
tools/methydackel.cwl
(CommandLineTool)
|
||
| bwameth_align |
tools/bwameth_align.cwl
(CommandLineTool)
|
||
| merge_and_sort |
../../tools/samtools_merge_and_sort.cwl
(CommandLineTool)
|
||
| picard_markdup |
../../tools/picard_markdup.cwl
(CommandLineTool)
|
||
| samtools_index |
../../tools/samtools_index.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| call | File | ||
| bam_sorted_indexed | File | ||
| picard_markdup_log | File | ||
| picard_markdup_stat | File |
Permalink:
https://w3id.org/cwl/view/git/1416ade270d1b990087e39c6680464c12cf564cc/workflows/bwameth/bwameth_singlelib.cwl
