Workflow: qc_workflow_wo_waltz.cwl
Fetched 2024-05-18 11:11:10 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 |
|---|---|---|---|
| title_file | File | ||
| inputs_yaml | File | ||
| FP_config_file | File | ||
| 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 |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| combine_qc |
../../cwl_tools/python/combine_qc_pdfs.cwl
(CommandLineTool)
|
||
| noise_plots |
../../cwl_tools/noise/plot_noise.cwl
(CommandLineTool)
|
||
| noise_tables |
../../cwl_tools/noise/calculate_noise.cwl
(CommandLineTool)
|
||
| innovation_qc |
../../cwl_tools/python/innovation_qc.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 |
|
| duplex_aggregate_bam_metrics_pool_a |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
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||
| 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)
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||
| simplex_aggregate_bam_metrics_pool_b |
../../cwl_tools/python/aggregate_bam_metrics.cwl
(CommandLineTool)
|
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| 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)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| combined_qc | Directory |
Permalink:
https://w3id.org/cwl/view/git/f874bd8a9bb7da9839f0aa6be708d5d16f72945d/workflows/QC/qc_workflow_wo_waltz.cwl
