Workflow: qc_simplex_bam
Fetched 2023-01-03 22:49:04 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 |
|---|---|---|---|
| reference | File | ||
| simplex_bam | File | simplex_bam | |
| pool_a_bait_intervals | File | pool_a_bait_intervals | |
| pool_b_bait_intervals | File | pool_b_bait_intervals | |
| hsmetrics_coverage_cap | Integer (Optional) | ||
| pool_a_target_intervals | File | pool_a_target_intervals | |
| pool_b_target_intervals | File | pool_b_target_intervals | |
| hsmetrics_minimum_base_quality | Integer (Optional) | ||
| hsmetrics_minimum_mapping_quality | Integer (Optional) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| bam_qc_stats_pool_a |
access_qc__packed.cwl#bam_qc_stats.cwl
(Workflow)
|
bam_qc_stats | |
| bam_qc_stats_pool_b |
access_qc__packed.cwl#bam_qc_stats.cwl
(Workflow)
|
bam_qc_stats |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| gatk_collect_hs_metrics_txt_pool_a | File | gatk_collect_hs_metrics_txt_pool_a | |
| gatk_collect_hs_metrics_txt_pool_b | File | gatk_collect_hs_metrics_txt_pool_b | |
| gatk_collect_insert_size_metrics_txt_pool_a | File | gatk_collect_insert_size_metrics_txt_pool_a | |
| gatk_collect_insert_size_metrics_txt_pool_b | File | gatk_collect_insert_size_metrics_txt_pool_b | |
| gatk_collect_alignment_summary_metrics_txt_pool_a | File | gatk_collect_alignment_summary_metrics_txt_pool_a | |
| gatk_collect_alignment_summary_metrics_txt_pool_b | File | gatk_collect_alignment_summary_metrics_txt_pool_b | |
| gatk_collect_hs_metrics_per_base_coverage_txt_pool_a | File | gatk_collect_hs_metrics_per_base_coverage_txt_pool_a | |
| gatk_collect_hs_metrics_per_base_coverage_txt_pool_b | File | gatk_collect_hs_metrics_per_base_coverage_txt_pool_b | |
| gatk_collect_insert_size_metrics_histogram_pdf_pool_a | File | gatk_collect_insert_size_metrics_histogram_pdf_pool_a | |
| gatk_collect_insert_size_metrics_histogram_pdf_pool_b | File | gatk_collect_insert_size_metrics_histogram_pdf_pool_b | |
| gatk_collect_hs_metrics_per_target_coverage_txt_pool_a | File | gatk_collect_hs_metrics_per_target_coverage_txt_pool_a | |
| gatk_collect_hs_metrics_per_target_coverage_txt_pool_b | File | gatk_collect_hs_metrics_per_target_coverage_txt_pool_b |
Permalink:
https://w3id.org/cwl/view/git/248e7c3edaff48e1b97a7931d66aa3b23ce97f54/access_qc__packed.cwl?part=qc_simplex_bam.cwl
