Workflow: qc_workflow_wo_waltz.cwl
Fetched 2024-05-18 19:02:55 GMT
Verified with cwltool version 3.1.20230201224320
This workflow is intended to be used to test the QC module, without having to run the long waltz step
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| hotspots | File | ||
| run_tools | https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/resources/schemas/collapsing_tools.yaml#run_tools | ||
| sample_id | String[] | ||
| patient_id | String[] | ||
| title_file | File | ||
| inputs_yaml | File | ||
| project_name | String | ||
| sample_class | String[] | ||
| FP_config_file | File | ||
| picard_metrics | Directory | ||
| sample_directories | Directory[] | ||
| waltz_duplex_pool_a | Directory | ||
| waltz_duplex_pool_b | Directory | ||
| waltz_simplex_pool_a | Directory | ||
| waltz_simplex_pool_b | Directory | ||
| A_on_target_positions | File | ||
| B_on_target_positions | File | ||
| waltz_standard_pool_a | Directory | ||
| waltz_standard_pool_b | Directory | ||
| noise__good_positions_A | File | ||
| waltz_unfiltered_pool_a | Directory | ||
| waltz_unfiltered_pool_b | Directory | ||
| waltz_duplex_pool_a_pileups | File[] | ||
| waltz_duplex_a_exon_level_files | Directory | ||
| waltz_unfiltered_pool_a_pileups | File[] | ||
| waltz_simplex_a_exon_level_files | Directory | ||
| waltz_standard_a_exon_level_files | Directory | ||
| waltz_unfiltered_a_exon_level_files | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| combine_qc |
../../cwl_tools/python/combine_qc_pdfs.cwl
(CommandLineTool)
|
||
| umi_qc_tables |
../../cwl_tools/umi_qc/make_umi_qc_tables.cwl
(CommandLineTool)
|
||
| fingerprinting |
../../cwl_tools/python/fingerprinting.cwl
(CommandLineTool)
|
||
| group_qc_files |
../../cwl_tools/expression_tools/group_qc_files.cwl
(ExpressionTool)
|
This tool groups waltz qc files into a single directory |
|
| base_quality_plot |
../../cwl_tools/python/base_quality_plot.cwl
(CommandLineTool)
|
||
| main_plots_module |
../../cwl_tools/python/plots_module.cwl
(CommandLineTool)
|
||
| main_tables_module |
../../cwl_tools/python/tables_module.cwl
(CommandLineTool)
|
||
| duplex_noise_plots_A |
../../cwl_tools/noise/plot_noise.cwl
(CommandLineTool)
|
||
| duplex_noise_tables_A |
../../cwl_tools/noise/calculate_noise.cwl
(CommandLineTool)
|
||
| simplex_noise_plots_A |
../../cwl_tools/noise/plot_noise.cwl
(CommandLineTool)
|
||
| simplex_noise_tables_A |
../../cwl_tools/noise/calculate_noise.cwl
(CommandLineTool)
|
||
| standard_noise_plots_A |
../../cwl_tools/noise/plot_noise.cwl
(CommandLineTool)
|
||
| standard_noise_tables_A |
../../cwl_tools/noise/calculate_noise.cwl
(CommandLineTool)
|
||
| find_hotspots_in_normals |
../subworkflows/find_hotspots_in_normals.cwl
(Workflow)
|
Workflow to find hotspot VAFs from duplex (for Tumor sample) and unfiltered (for Normal sample) pileups. |
|
| unfiltered_noise_plots_A |
../../cwl_tools/noise/plot_noise.cwl
(CommandLineTool)
|
||
| unfiltered_noise_tables_A |
../../cwl_tools/noise/calculate_noise.cwl
(CommandLineTool)
|
||
| duplex_aggregate_bam_metrics_pool_a |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| duplex_aggregate_bam_metrics_pool_b |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| simplex_aggregate_bam_metrics_pool_a |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| simplex_aggregate_bam_metrics_pool_b |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| standard_aggregate_bam_metrics_pool_a |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| standard_aggregate_bam_metrics_pool_b |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| unfiltered_aggregate_bam_metrics_pool_a |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| unfiltered_aggregate_bam_metrics_pool_b |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| duplex_aggregate_bam_metrics_pool_a_exon_level |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| simplex_aggregate_bam_metrics_pool_a_exon_level |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| standard_aggregate_bam_metrics_pool_a_exon_level |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
||
| unfiltered_aggregate_bam_metrics_pool_a_exon_level |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| tables | Directory | ||
| combined_qc | Directory | ||
| hotspots_in_normals_data | File |
Permalink:
https://w3id.org/cwl/view/git/b0f226a9ac5152f3afe0d38c8cd54aa25b8b01cf/workflows/QC/qc_workflow_wo_waltz.cwl
