Workflow: qc_generator
Fetched 2023-01-03 22:58:20 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 |
|---|---|---|---|
| vcf_file | File | ||
| reference | File | ||
| duplex_bam | File | duplex_bam | |
| sample_sex | String (Optional) |
Expected sample sex (i.e. M or F). |
|
| sample_name | String (Optional) |
Sample name. If not specified, sample name is automatically figured out from the BAM file. |
|
| simplex_bam | File | simplex_bam | |
| hotspots_maf | File | ||
| sample_group | String |
The sample group (e.g. the sample patient ID). |
|
| collapsed_bam | File | collapsed_bam | |
| biometrics_json | Boolean (Optional) | biometrics_json |
Also output data in JSON format. |
| biometrics_plot | Boolean (Optional) | biometrics_plot |
Also output plots of the data. |
| 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) | ||
| group_reads_by_umi_bam | File | group_reads_by_umi_bam |
Input BAM file generated by GroupReadByUmi. |
| 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 |
An aligned SAM or BAM file. Required. |
| hsmetrics_minimum_base_quality | Integer (Optional) | ||
| duplex_biometrics_major_threshold | Float (Optional) | duplex_biometrics_major_threshold |
Major contamination threshold for bad sample. |
| hsmetrics_minimum_mapping_quality | Integer (Optional) | ||
| collapsed_biometrics_minor_threshold | Float (Optional) | collapsed_biometrics_minor_threshold |
Minor contamination threshold for bad sample. |
| collapsed_biometrics_coverage_threshold | Integer (Optional) | collapsed_biometrics_coverage_threshold |
Samples with Y chromosome above this value will be considered male. |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc_duplex_bam |
access_qc__packed.cwl#qc_duplex_bam.cwl
(Workflow)
|
qc_duplex | |
| qc_simplex_bam |
access_qc__packed.cwl#qc_simplex_bam.cwl
(Workflow)
|
qc_simplex_bam | |
| qc_collapsed_bam |
access_qc__packed.cwl#qc_collapsed_bam.cwl
(Workflow)
|
qc_collapsed_bam | |
| qc_uncollapsed_bam |
access_qc__packed.cwl#qc_uncollapsed_bam.cwl
(Workflow)
|
qc_uncollapsed_bam | |
| simplex_bam_pool_a |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| simplex_bam_pool_b |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_bam_biometrics |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_bam_sequence_qc |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_bam_stats_pool_a |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| duplex_bam_stats_pool_b |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_bam_biometrics |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_bam_stats_pool_a |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_bam_stats_pool_b |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| uncollapsed_bam_stats_pool_a |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| uncollapsed_bam_stats_pool_b |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| gatk_mean_quality_by_cycle_recal |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_bam_duplex_metrics_pool_a |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
||
| collapsed_bam_duplex_metrics_pool_b |
access_qc__packed.cwl#put_in_dir.cwl
(ExpressionTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| simplex_bam_pool_a_dir | Directory | simplex_bam_pool_a_dir | |
| simplex_bam_pool_b_dir | Directory | simplex_bam_pool_b_dir | |
| duplex_bam_biometrics_dir | Directory | duplex_bam_biometrics_dir | |
| duplex_bam_genotyping_maf | File | duplex_bam_genotyping_maf | |
| 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_biometrics_dir | Directory | collapsed_bam_biometrics_dir | |
| collapsed_bam_genotyping_maf | File | ||
| 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 | |
| duplex_biometrics_extract_pickle | File | ||
| 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 | |
| collapsed_biometrics_extract_pickle | File | ||
| 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 |
Permalink:
https://w3id.org/cwl/view/git/248e7c3edaff48e1b97a7931d66aa3b23ce97f54/access_qc__packed.cwl?part=qc_generator.cwl
