Workflow: Detect Variants workflow
Fetched 2024-06-09 06:08:57 GMT
Verified with cwltool version 3.1.20230201224320
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- Inputs/Outputs
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| vep_pick | |||
| reference | File | ||
| sample_bam | File | ||
| sample_name | String | ||
| vep_plugins | String[] | ||
| min_coverage | Integer (Optional) | ||
| min_var_freq | Float (Optional) | ||
| roi_intervals | File |
roi_intervals is a list of regions (in interval_list format) within which to call somatic variants |
|
| scatter_count | Integer (Optional) |
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs. |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| whitelist_vcf | File |
Whitelisted variants (VCF) and accompanying .tbi file. |
|
| cle_vcf_filter | Boolean | ||
| known_variants | File (Optional) |
Previously discovered variants to be flagged in this pipelines's output vcf |
|
| varscan_p_value | Float (Optional) | ||
| pindel_insert_size | Integer | ||
| strelka_exome_mode | Boolean (Optional) | ||
| matched_control_bam | File | ||
| vep_ensembl_species | String |
ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus |
|
| vep_ensembl_version | String |
ensembl version - Must be present in the cache directory. Example: 95 |
|
| vep_to_table_fields | String[] | ||
| annotate_coding_only | Boolean (Optional) | ||
| filter_minimum_depth | Integer | ||
| matched_control_name | String | ||
| panel_of_normal_bams | File[] | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| varscan_strand_filter | Integer (Optional) | ||
| filter_mapq0_threshold | Float | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| filter_whitelist_variants | Boolean |
Determines whether variants found only via genotyping of whitelist sites will be filtered (as WHITELIST_ONLY) or passed through as variant calls |
|
| readcount_minimum_base_quality | Integer (Optional) | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] | ||
| filter_gnomADe_maximum_population_allele_frequency | Float |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| mutect |
../subworkflows/mutect.cwl
(Workflow)
|
mutect parallel workflow | |
| pindel |
../subworkflows/pindel.cwl
(Workflow)
|
pindel parallel workflow | |
| combine |
../tools/combine_variants.cwl
(CommandLineTool)
|
Combine variants from multiple vcfs | |
| strelka | strelka workflow | ||
| varscan | Varscan Workflow | ||
| decompose |
../tools/vt_decompose.cwl
(CommandLineTool)
|
run vt decompose | |
| whitelist |
../subworkflows/whitelist.cwl
(Workflow)
|
Detect whitelisted variants | |
| filter_vcf |
../subworkflows/filter_vcf.cwl
(Workflow)
|
Apply filters to VCF file | |
| combined_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| combined_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| decompose_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| annotate_variants |
../tools/vep.cwl
(CommandLineTool)
|
Ensembl Variant Effect Predictor | |
| variants_to_table |
../tools/variants_to_table.cwl
(CommandLineTool)
|
SelectVariants (GATK 4.1.8.1) | |
| add_filter_to_info |
../tools/add_filter_to_info.cwl
(CommandLineTool)
|
Add FILTER column info to INFO column | |
| set_final_tsv_name |
../tools/staged_rename.cwl
(CommandLineTool)
|
Staged Renamer |
Renames a file by staging and then `mv`ing it. A workaround for workflow engines that don't support rename.cwl. If running in cwltool, use the other one instead. |
| tumor_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| normal_bam_readcount |
../tools/bam_readcount.cwl
(CommandLineTool)
|
run bam-readcount | |
| add_comments_to_table |
../tools/add_comments_to_table.cwl
(CommandLineTool)
|
Add useful comments to table output | |
| annotated_filter_bgzip |
../tools/bgzip.cwl
(CommandLineTool)
|
bgzip VCF | |
| annotated_filter_index |
../tools/index_vcf.cwl
(CommandLineTool)
|
vcf index | |
| add_vep_fields_to_table |
../tools/add_vep_fields_to_table.cwl
(CommandLineTool)
|
add VEP annotation to report | |
| background_error_suppression | SNV background error suppression using panel of normals | ||
| add_tumor_bam_readcount_to_vcf |
../subworkflows/vcf_readcount_annotator.cwl
(Workflow)
|
Add snv and indel bam-readcount files to a vcf | |
| add_normal_bam_readcount_to_vcf |
../subworkflows/vcf_readcount_annotator.cwl
(Workflow)
|
Add snv and indel bam-readcount files to a vcf |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_tsv | File | ||
| final_vcf | File | ||
| vep_summary | File | ||
| final_filtered_vcf | File | ||
| mutect_filtered_vcf | File | ||
| pindel_filtered_vcf | File | ||
| strelka_filtered_vcf | File | ||
| varscan_filtered_vcf | File | ||
| mutect_unfiltered_vcf | File | ||
| pindel_unfiltered_vcf | File | ||
| strelka_unfiltered_vcf | File | ||
| varscan_unfiltered_vcf | File | ||
| whitelist_filtered_vcf | File | ||
| tumor_snv_bam_readcount_tsv | File | ||
| normal_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File | ||
| normal_indel_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/656d9ae18f164f983c5672bcf51037cd73309f4f/pipelines/snv_indel_post_processing.cwl
