Workflow: module-1
Fetched 2023-01-03 19:56:25 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 |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| genome | String | ||
| adapter | String | ||
| tmp_dir | String | ||
| adapter2 | String | ||
| add_rg_CN | String | ||
| add_rg_ID | String | ||
| add_rg_LB | String | ||
| add_rg_PL | String | ||
| add_rg_PU | String | ||
| add_rg_SM | String | ||
| md_output | String | ||
| bwa_output | String | ||
| add_rg_output | String | ||
| md_metrics_output | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| cmo-bwa-mem |
cmo-bwa-mem/0.7.5a/cmo-bwa-mem.cwl
(CommandLineTool)
|
cmo-bwa-mem |
run bwa mem |
| cmo-trimgalore |
cmo-trimgalore/0.2.5.mod/cmo-trimgalore.cwl
(CommandLineTool)
|
cmo-trimgalore |
None |
| cmo-picard.MarkDuplicates |
cmo-picard.MarkDuplicates/2.9/cmo-picard.MarkDuplicates.cwl
(CommandLineTool)
|
cmo-picard-MarkDuplicates |
None |
| cmo-picard.AddOrReplaceReadGroups |
cmo-picard.AddOrReplaceReadGroups/2.9/cmo-picard.AddOrReplaceReadGroups.cwl
(CommandLineTool)
|
cmo-picard-AddOrReplaceReadGroups |
None |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bai | File | ||
| bam | File | ||
| clstats1 | File | ||
| clstats2 | File | ||
| md_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/3ec29bfdcbc444c6599e484640cf83a7c5d91aaa/setup/cwl/module-1.cwl
