Workflow: wgs alignment and germline variant detection
Fetched 2023-01-05 01:53:47 GMT
Verified with cwltool version 3.1.20221201130942
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- |
- Default Values
- Nested Workflows
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- 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 |
|---|---|---|---|
| bams | File[] | ||
| mills | File | ||
| omni_vcf | File | ||
| dbsnp_vcf | File | ||
| intervals | 92cecd3688476494c2d851f65a07cf7c[] | ||
| reference | String | ||
| readgroups | String[] | ||
| coding_only | Boolean (Optional) | ||
| known_indels | File | ||
| qc_intervals | File | ||
| cnvkit_method | String (Optional) | ||
| gvcf_gq_bands | String[] | ||
| manta_non_wgs | Boolean (Optional) | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| bqsr_intervals | String[] (Optional) | ||
| cnvkit_diagram | Boolean (Optional) | ||
| cnvkit_vcf_name | String (Optional) | ||
| custom_gnomad_vcf | File (Optional) | ||
| summary_intervals | https://w3id.org/cwl/view/git/5c49c5a53259d4c88a02750f1a16a3c02d711115/definitions/types/labelled_file.yml#labelled_file[] | ||
| custom_clinvar_vcf | File (Optional) | ||
| manta_call_regions | File (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/5c49c5a53259d4c88a02750f1a16a3c02d711115/definitions/types/labelled_file.yml#labelled_file[] | ||
| cnvkit_scatter_plot | Boolean (Optional) | ||
| cnvkit_reference_cnn | File | ||
| manta_output_contigs | Boolean (Optional) | ||
| minimum_base_quality | Integer (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/5c49c5a53259d4c88a02750f1a16a3c02d711115/definitions/types/labelled_file.yml#labelled_file[] | ||
| cnvkit_male_reference | Boolean (Optional) | ||
| smoove_exclude_regions | File (Optional) | ||
| minimum_mapping_quality | Integer (Optional) | ||
| cnvkit_drop_low_coverage | Boolean (Optional) | ||
| emit_reference_confidence | String | ||
| variant_reporting_intervals | File | ||
| picard_metric_accumulation_level | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index_cram |
../tools/index_cram.cwl
(CommandLineTool)
|
samtools index cram | |
| bam_to_cram |
../tools/bam_to_cram.cwl
(CommandLineTool)
|
BAM to CRAM conversion | |
| detect_variants |
../subworkflows/germline_detect_variants.cwl
(Workflow)
|
exome alignment and germline variant detection | |
| extract_freemix |
germline_wgs.cwl#extract_freemix/7e1d9983-6b7a-4667-929f-f429e89040fd
(ExpressionTool)
|
||
| variant_callers |
../subworkflows/single_sample_sv_callers.cwl
(Workflow)
|
Subworkflow to allow calling different SV callers which require bam files as inputs | |
| alignment_and_qc |
wgs_alignment.cwl
(Workflow)
|
wgs alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| gvcf | File[] | ||
| final_vcf | File | ||
| flagstats | File | ||
| cn_diagram | File (Optional) | ||
| cnvkit_vcf | File | ||
| coding_vcf | File | ||
| limited_vcf | File | ||
| vep_summary | File | ||
| wgs_metrics | File | ||
| cn_scatter_plot | File (Optional) | ||
| 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 | ||
| manta_all_candidates | File | ||
| gc_bias_metrics_chart | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| tumor_target_coverage | File | ||
| verify_bam_id_metrics | File | ||
| manta_diploid_variants | File (Optional) | ||
| manta_small_candidates | File | ||
| manta_somatic_variants | File (Optional) | ||
| smoove_output_variants | File | ||
| tumor_bin_level_ratios | File | ||
| tumor_segmented_ratios | File | ||
| gc_bias_metrics_summary | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| manta_tumor_only_variants | File (Optional) | ||
| per_base_coverage_metrics | File[] | ||
| tumor_antitarget_coverage | File | ||
| per_target_coverage_metrics | File[] |
Permalink:
https://w3id.org/cwl/view/git/5c49c5a53259d4c88a02750f1a16a3c02d711115/definitions/pipelines/germline_wgs.cwl
