Workflow: metrics.cwl
Fetched 2023-01-11 22:53:05 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 |
|---|---|---|---|
| bam | File | ||
| uuid | String | ||
| fasta | File | ||
| db_snp_vcf | File | ||
| parent_bam | String | ||
| input_state | String | ||
| thread_count | Integer |
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/53fd4d4c05891c7c8b5cd6a5a8179a08c2e585c9/workflows/dnaseq/metrics.cwl
