Workflow: module-1.cwl
Fetched 2023-01-25 00:27:18 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File | ||
| fastq2 | File | ||
| tmp_dir | 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 | |||
| trim__gzip | Boolean | ||
| trim__length | Integer | ||
| trim__paired | Boolean | ||
| trim__quality | Integer | ||
| reference_fasta | String | ||
| md__create_index | Boolean | ||
| trim__stringency | Integer | ||
| md__assume_sorted | Boolean | ||
| reference_fasta_fai | String | ||
| trim__suppress_warn | Boolean | ||
| md__compression_level | Integer | ||
| md__validation_stringency | String | ||
| md__duplicate_scoring_strategy | String |
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/e7754fb4d3cd14068eef0c498cc5c6fcf53dc31f/workflows/module-1.cwl
