Workflow: module-1-scatter-chunk
Fetched 2023-01-04 06:20:09 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 |
|---|---|---|---|
| group | String | ||
| fastq1 | String[] | ||
| fastq2 | String[] | ||
| 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 | ||
| bwa_output | String | ||
| opt_dup_pix_dist | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| align | |||
| flatten |
flatten-array/1.0.0/flatten-array-fastq.cwl
(ExpressionTool)
|
flatten-array-fastq | |
| chunking |
cmo-split-reads/1.0.1/cmo-split-reads.cwl
(CommandLineTool)
|
cmo-split-reads |
split files into chunks based on filesize |
| mark_duplicates |
cmo-picard.MarkDuplicates/2.9/cmo-picard.MarkDuplicates.cwl
(CommandLineTool)
|
cmo-picard-MarkDuplicates |
None |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| clstats1 | File[] | ||
| clstats2 | File[] | ||
| md_metrics | File |
Permalink:
https://w3id.org/cwl/view/git/7a2864f5af7723657406e4f3e94f92db09ec90fc/setup/cwl/module-1.scatter.chunk.cwl
