Workflow: metrics.cwl
Fetched 2024-04-18 20:05:15 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 |
|---|---|---|---|
| bam | File | ||
| fasta | File | ||
| job_uuid | String | ||
| known_snp | File | ||
| parent_bam | String | ||
| input_state | String | ||
| thread_count | Long |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| merge_sqlite |
../../tools/merge_sqlite.cwl
(CommandLineTool)
|
||
| samtools_stats |
../../tools/samtools_stats.cwl
(CommandLineTool)
|
||
| samtools_flagstat |
../../tools/samtools_flagstat.cwl
(CommandLineTool)
|
||
| samtools_idxstats |
../../tools/samtools_idxstats.cwl
(CommandLineTool)
|
||
| picard_collectwgsmetrics |
../../tools/picard_collectwgsmetrics.cwl
(CommandLineTool)
|
||
| samtools_stats_to_sqlite |
../../tools/samtools_stats_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_collectoxogmetrics |
../../tools/picard_collectoxogmetrics.cwl
(CommandLineTool)
|
||
| samtools_flagstat_to_sqlite |
../../tools/samtools_flagstat_to_sqlite.cwl
(CommandLineTool)
|
||
| samtools_idxstats_to_sqlite |
../../tools/samtools_idxstats_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_collectmultiplemetrics |
../../tools/picard_collectmultiplemetrics.cwl
(CommandLineTool)
|
||
| picard_collectwgsmetrics_to_sqlite |
../../tools/picard_collectwgsmetrics_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_collectoxogmetrics_to_sqlite |
../../tools/picard_collectoxogmetrics_to_sqlite.cwl
(CommandLineTool)
|
||
| picard_collectmultiplemetrics_to_sqlite |
../../tools/picard_collectmultiplemetrics_to_sqlite.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| merge_sqlite_destination_sqlite | File |
Permalink:
https://w3id.org/cwl/view/git/58af8583ab04b8836777745a2116a2e79f9b441b/workflows/dnaseq/metrics.cwl
