Workflow: wgs alignment with qc
Fetched 2023-01-10 22:56:23 GMT
Verified with cwltool version 3.1.20221201130942
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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 |
|---|---|---|---|
| omni_vcf | File | ||
| sequence | https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/sequence_data.yml#sequence_data[] | sequence: sequencing data and readgroup information |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| trimming | https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/trimming_options.yml#trimming_options (Optional) | ||
| intervals | File | ||
| reference | File | ||
| sample_name | String (Optional) | ||
| bqsr_intervals | String[] (Optional) | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| summary_intervals | https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[] | ||
| per_base_intervals | https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/types/labelled_file.yml#labelled_file[] | ||
| minimum_mapping_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| qc |
../subworkflows/qc_wgs.cwl
(Workflow)
|
WGS QC workflow | |
| alignment |
../subworkflows/sequence_to_bqsr.cwl
(Workflow)
|
Raw sequence data to BQSR |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| flagstats | File | ||
| wgs_metrics | File | ||
| gc_bias_metrics | 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 | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/93656ed6582073e434eab168c610625a835dce37/definitions/pipelines/alignment_wgs.cwl
