Workflow: qc_uncollapsed_bam
Fetched 2023-01-04 18:49:06 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 | ||
| 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 | |
| uncollapsed_bam_base_recal | File[] | uncollapsed_bam_base_recal | |
| 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 | |
| gatk_revert_sam_4_1_8_0 |
access_qc__packed.cwl#gatk_revert_sam_4.1.8.0.cwl
(CommandLineTool)
|
GATK-RevertSam | |
| gatk_mean_quality_by_cycle_4_1_8_1 |
access_qc__packed.cwl#gatk_mean_quality_by_cycle_4.1.8.0.cwl
(CommandLineTool)
|
GATK-MeanQualityByCycle |
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_mean_quality_by_cycle_output_base_recal | File[] | gatk_mean_quality_by_cycle_output_base_recal | |
| 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_mean_quality_by_cycle_chart_output_base_recal | File[] | gatk_mean_quality_by_cycle_chart_output_base_recal | |
| 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_uncollapsed_bam.cwl
