Workflow: bam_qc_stats
Fetched 2024-05-07 05:41:07 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
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- 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 |
|---|---|---|---|
| input | File[] | ||
| reference | File | ||
| bait_intervals | File | ||
| target_intervals | File | ||
| temporary_directory | String (Optional) | ||
| hsmetrics_coverage_cap | Integer (Optional) | hsmetrics_coverage_cap | |
| hsmetrics_minimum_base_quality | Integer (Optional) | hsmetrics_minimum_base_quality | |
| hsmetrics_minimum_mapping_quality | Integer (Optional) | hsmetrics_minimum_mapping_quality |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| gatk_collect_hs_metrics_4_1_8_0 |
access_qc__packed.cwl#gatk_collect_hs_metrics_4.1.8.0.cwl
(CommandLineTool)
|
GATK-CollectHsMetrics | |
| gatk_collect_insert_size_metrics_4_1_8_0 |
access_qc__packed.cwl#gatk_collect_insert_size_metrics_4.1.8.0.cwl
(CommandLineTool)
|
GATK-CollectInsertSizeMetrics | |
| gatk_collect_alignment_summary_metrics_4_1_3_0 |
access_qc__packed.cwl#gatk_collect_alignment_summary_metrics_4.1.8.0.cwl
(CommandLineTool)
|
GATK-CollectAlignmentSummaryMetrics |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatk_collect_hs_metrics_txt | File[] | ||
| gatk_collect_insert_size_metrics_txt | File[] | ||
| gatk_collect_alignment_summary_metrics_txt | File[] | ||
| gatk_collect_hs_metrics_per_base_coverage_txt | File[] | ||
| gatk_collect_insert_size_metrics_histogram_pdf | File[] | ||
| gatk_collect_hs_metrics_per_target_coverage_txt | File[] |
Permalink:
https://w3id.org/cwl/view/git/248e7c3edaff48e1b97a7931d66aa3b23ce97f54/access_qc__packed.cwl?part=bam_qc_stats.cwl
