Workflow: module-1.cwl
Fetched 2024-05-03 19:42:04 GMT
Verified with cwltool version 3.1.20230127121939
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| adapter | String | ||
| adapter2 | String | ||
| add_rg_CN | String | ||
| add_rg_ID | String | ||
| add_rg_LB | Integer | ||
| add_rg_PL | String | ||
| add_rg_PU | String | ||
| add_rg_SM | String | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| reference_fasta | String | ||
| trimgalore__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/trimgalore.yaml#trimgalore__params | ||
| reference_fasta_fai | String | ||
| mark_duplicates__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/mark_duplicates.yaml#mark_duplicates__params | ||
| add_or_replace_read_groups__params | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/params/add_or_replace_read_groups.yaml#add_or_replace_read_groups__params |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bwa_mem |
../cwl_tools/bwa-mem/bwa-mem.cwl
(CommandLineTool)
|
||
| trimgalore |
../cwl_tools/trimgalore/trimgalore.cwl
(CommandLineTool)
|
None |
|
| picard.MarkDuplicates |
../cwl_tools/picard/MarkDuplicates.cwl
(CommandLineTool)
|
None |
|
| picard.AddOrReplaceReadGroups |
../cwl_tools/picard/AddOrReplaceReadGroups.cwl
(CommandLineTool)
|
None |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bai | File | ||
| bam | File | ||
| clstats1 | File | ||
| clstats2 | File | ||
| md_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/module-1.cwl
