Workflow: qc_aggregator
Fetched 2023-01-09 22:05:19 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| biometrics_json | Boolean (Optional) | biometrics_json |
Also output data in JSON format. |
| biometrics_plot | Boolean (Optional) | biometrics_plot |
Also output plots of the data. |
| biometrics_threads | Integer (Optional) | biometrics_threads |
Number of threads to use. |
| simplex_bam_pool_a_dir | Directory[] | simplex_bam_pool_a_dir | |
| simplex_bam_pool_b_dir | Directory[] | simplex_bam_pool_b_dir | |
| duplex_extraction_files | File[] | duplex_extraction_files |
Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once. |
| collapsed_extraction_files | File[] | collapsed_extraction_files |
Can be one of three types: (1) path to a CSV file containing sample information (one per line). For example: sample_name,sample_bam,sample_type,sample_sex,sample_group. (2) Path to a '*.pk' file that was produced by the 'extract' tool. (3) Name of the sample to analyze; this assumes there is a file named '{sample_name}.pk' in your database directory. Can be specified more than once. |
| duplex_bam_sequence_qc_dir | Directory[] | duplex_bam_sequence_qc_dir | |
| duplex_bam_stats_pool_a_dir | Directory[] | duplex_bam_stats_pool_a_dir | |
| duplex_bam_stats_pool_b_dir | Directory[] | duplex_bam_stats_pool_b_dir | |
| collapsed_bam_stats_pool_a_dir | Directory[] | collapsed_bam_stats_pool_a_dir | |
| collapsed_bam_stats_pool_b_dir | Directory[] | collapsed_bam_stats_pool_b_dir | |
| uncollapsed_bam_stats_pool_a_dir | Directory[] | uncollapsed_bam_stats_pool_a_dir | |
| uncollapsed_bam_stats_pool_b_dir | Directory[] | uncollapsed_bam_stats_pool_b_dir | |
| duplex_biometrics_major_threshold | Float (Optional) | duplex_biometrics_major_threshold |
Major contamination threshold for bad sample. |
| duplex_biometrics_minor_threshold | Float (Optional) | duplex_biometrics_minor_threshold |
Minor contamination threshold for bad sample. |
| collapsed_biometrics_major_threshold | Float (Optional) | collapsed_biometrics_major_threshold |
Major contamination threshold for bad sample. |
| collapsed_biometrics_minor_threshold | Float (Optional) | collapsed_biometrics_minor_threshold |
Minor contamination threshold for bad sample. |
| gatk_mean_quality_by_cycle_recal_dir | Directory[] | gatk_mean_quality_by_cycle_recal_dir | |
| collapsed_bam_duplex_metrics_pool_a_dir | Directory[] | collapsed_bam_duplex_metrics_pool_a_dir | |
| collapsed_bam_duplex_metrics_pool_b_dir | Directory[] | collapsed_bam_duplex_metrics_pool_b_dir | |
| collapsed_biometrics_coverage_threshold | Integer (Optional) | collapsed_biometrics_coverage_threshold |
Samples with Y chromosome above this value will be considered male. |
| duplex_biometrics_discordance_threshold | Float (Optional) |
Discordance values less than this are regarded as matching samples. (default: 0.05) |
|
| collapsed_biometrics_discordance_threshold | Float (Optional) | collapsed_biometrics_discordance_threshold |
Discordance values less than this are regarded as matching samples. (default: 0.05) |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| aggregate |
aggregate_visualize__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| final_aggregate |
aggregate_visualize__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_biometrics_agg |
aggregate_visualize__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_biometrics_major |
aggregate_visualize__packed.cwl#biometrics_major.cwl
(CommandLineTool)
|
||
| duplex_biometrics_minor |
aggregate_visualize__packed.cwl#biometrics_minor.cwl
(CommandLineTool)
|
||
| collapsed_biometrics_agg |
aggregate_visualize__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_biometrics_major |
aggregate_visualize__packed.cwl#biometrics_major.cwl
(CommandLineTool)
|
||
| collapsed_biometrics_minor |
aggregate_visualize__packed.cwl#biometrics_minor.cwl
(CommandLineTool)
|
||
| duplex_biometrics_genotype |
aggregate_visualize__packed.cwl#biometrics_genotype.cwl
(CommandLineTool)
|
||
| collapsed_biometrics_genotype |
aggregate_visualize__packed.cwl#biometrics_genotype.cwl
(CommandLineTool)
|
||
| collapsed_biometrics_sexmismatch |
aggregate_visualize__packed.cwl#biometrics_sexmismatch.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| aggregate_qc_stats | Directory | aggregate_qc_stats |
https://w3id.org/cwl/view/git/248e7c3edaff48e1b97a7931d66aa3b23ce97f54/aggregate_visualize__packed.cwl?part=qc_aggregator.cwl
