Workflow: harmonization_novoalign.cwl
Fetched 2023-01-11 05:48:37 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:
Apache License 2.0
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dbname | File | ||
| job_uuid | String | ||
| input_bam | File | ||
| interval_bed | File | ||
| reference_fai_index | File |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bam_sort |
../../tools/harmonization/sambamba_sort.cwl
(CommandLineTool)
|
||
| bam_reheader |
../../tools/harmonization/samtools_filter_reheader.cwl
(CommandLineTool)
|
||
| bam_to_fastq |
../../tools/harmonization/bam_to_fastq.cwl
(CommandLineTool)
|
||
| trim_adaptor |
../../tools/harmonization/trimmomatic.cwl
(CommandLineTool)
|
||
| readgroups_merge |
../../tools/harmonization/sambamba_merge.cwl
(CommandLineTool)
|
||
| get_bam_new_header |
../../tools/harmonization/get_bam_new_header.cwl
(CommandLineTool)
|
||
| get_readgroup_info |
../../tools/harmonization/get_readgroup_name.cwl
(CommandLineTool)
|
||
| novoalign_filter_dedup |
../../tools/harmonization/novoalign.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| sorted_bam | File | ||
| time_metrics_from_sort | File | ||
| time_metrics_from_merge | File | ||
| time_metrics_from_reheader | File | ||
| time_metrics_from_bam_to_fastq | File | ||
| time_metrics_from_trim_adaptor | File[] | ||
| time_metrics_from_novoalign_filter_dedup | File[] |
Permalink:
https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/cwl/workflows/harmonization/harmonization_novoalign.cwl
