Workflow: qc_duplex
Fetched 2024-11-27 04:31:28 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 |
|---|---|---|---|
| maf | File | ||
| json | Boolean (Optional) |
Also output data in JSON format. |
|
| plot | Boolean (Optional) |
Also output plots of the data. |
|
| prefix | String (Optional) | ||
| vcf_file | File | ||
| reference | File |
Path to reference fasta, containing all regions in bed_file |
|
| duplex_bam | File[] | duplex_bam | |
| sample_sex | String (Optional) | ||
| sample_name | String[] (Optional) |
Sample name. If not specified, sample name is automatically figured out from the BAM file. |
|
| sample_group | String (Optional) | ||
| major_threshold | Float (Optional) | ||
| noise_sites_bed | File | noise_sites_bed |
Path to BED file containing regions over which to calculate noise [required] |
| sequence_qc_min_basq | Integer (Optional) | ||
| sequence_qc_min_mapq | Integer (Optional) | ||
| sequence_qc_truncate | Integer (Optional) | ||
| pool_a_bait_intervals | File | pool_a_bait_intervals | |
| pool_b_bait_intervals | File | pool_b_bait_intervals | |
| sequence_qc_threshold | Float (Optional) | ||
| 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 |
|---|---|---|---|
| calculate_noise |
access_qc__packed.cwl#sequence_qc_0.2.3.cwl
(CommandLineTool)
|
||
| 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 | |
| biometrics_major_0_2_13 |
access_qc__packed.cwl#biometrics_major.cwl_2
(CommandLineTool)
|
||
| biometrics_minor_0_2_13 |
access_qc__packed.cwl#biometrics_minor.cwl_2
(CommandLineTool)
|
||
| biometrics_extract_0_2_13 |
access_qc__packed.cwl#biometrics_extract.cwl
(CommandLineTool)
|
||
| getbasecountsmultisample_1_2_5 |
access_qc__packed.cwl#getbasecountsmultisample_1.2.5.cwl
(CommandLineTool)
|
getbasecountsmultisample_1.2.5 |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| fillout_maf | File | ||
| sequence_qc_pileup | File[] | ||
| sequence_qc_figures | File[] | ||
| sequence_qc_noise_n | File[] | ||
| biometrics_major_csv | File | ||
| biometrics_minor_csv | File | ||
| biometrics_major_json | File (Optional) | ||
| biometrics_major_plot | File (Optional) | ||
| biometrics_minor_json | File (Optional) | ||
| biometrics_minor_plot | File (Optional) | ||
| sequence_qc_noise_del | File[] | ||
| sequence_qc_noise_acgt | File[] | ||
| biometrics_extract_pickle | File | ||
| biometrics_minor_sites_plot | File (Optional) | ||
| sequence_qc_noise_positions | File[] | ||
| sequence_qc_noise_by_substitution | File | ||
| 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_duplex_bam.cwl
