- 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 |
---|---|---|---|
bam | File | ||
omni_vcf | File | ||
intervals | File | ||
reference | File | ||
sample_name | String (Optional) | ||
summary_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
per_base_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
minimum_base_quality | Integer (Optional) | ||
per_target_intervals | https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/types/labelled_file.yml#labelled_file[] | ||
minimum_mapping_quality | Integer (Optional) | ||
picard_metric_accumulation_level | String |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
verify_bam_id |
../tools/verify_bam_id.cwl
(CommandLineTool)
|
verify BAM ID | |
samtools_flagstat |
../tools/samtools_flagstat.cwl
(CommandLineTool)
|
samtools flagstat | |
collect_hs_metrics |
hs_metrics.cwl
(Workflow)
|
HS Metrics workflow | |
collect_wgs_metrics |
../tools/collect_wgs_metrics.cwl
(CommandLineTool)
|
collect WGS metrics | |
cgpbigwig_bamcoverage |
../tools/bam_to_bigwig.cwl
(CommandLineTool)
|
cgpBigWig Converting BAM to BigWig | |
collect_gc_bias_metrics |
../tools/collect_gc_bias_metrics.cwl
(CommandLineTool)
|
collect gc bias metrics | |
collect_insert_size_metrics |
../tools/collect_insert_size_metrics.cwl
(CommandLineTool)
|
collect insert size metrics | |
collect_alignment_summary_metrics |
../tools/collect_alignment_summary_metrics.cwl
(CommandLineTool)
|
collect alignment summary metrics |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
flagstats | File | ||
wgs_metrics | File | ||
gc_bias_metrics | File | ||
bamcoverage_bigwig | File | ||
summary_hs_metrics | File[] | ||
insert_size_metrics | File | ||
per_base_hs_metrics | File[] | ||
verify_bam_id_depth | File | ||
gc_bias_metrics_chart | File | ||
insert_size_histogram | File | ||
per_target_hs_metrics | File[] | ||
verify_bam_id_metrics | File | ||
gc_bias_metrics_summary | File | ||
alignment_summary_metrics | File | ||
per_base_coverage_metrics | File[] | ||
per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/2e0562a5c3cd7aac24af4c622a5ae68a7fb23a71/definitions/subworkflows/qc_wgs.cwl