Workflow: exome alignment and tumor-only variant detection
Fetched 2023-01-09 22:10:09 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:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| mills | File | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| sequence | https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/types/sequence_data.yml#sequence_data[] | ||
| vep_pick | |||
| dbsnp_vcf | File | ||
| reference | File | ||
| sample_name | String | ||
| known_indels | File | ||
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | ||
| summary_intervals | https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/types/labelled_file.yml#labelled_file[] | ||
| varscan_min_reads | Integer (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/types/labelled_file.yml#labelled_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[] (Optional) | ||
| annotate_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/types/labelled_file.yml#labelled_file[] | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| vep_ensembl_assembly | String |
genome assembly to use in vep. Examples: GRCh38 or GRCm38 |
|
| varscan_strand_filter | Integer (Optional) | ||
| vep_custom_annotations | https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| variants_to_table_fields | String[] (Optional) | ||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| readcount_minimum_base_quality | Integer (Optional) | ||
| picard_metric_accumulation_level | String | ||
| readcount_minimum_mapping_quality | Integer (Optional) | ||
| variants_to_table_genotype_fields | String[] (Optional) | ||
| maximum_population_allele_frequency | Float (Optional) |
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 |
tumor_only_detect_variants.cwl
(Workflow)
|
Tumor-Only Detect Variants workflow | |
| alignment_and_qc |
alignment_exome.cwl
(Workflow)
|
exome alignment with qc |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| cram | File | ||
| final_tsv | File | ||
| final_vcf | File | ||
| flagstats | File | ||
| hs_metrics | File | ||
| varscan_vcf | File | ||
| vep_summary | File | ||
| annotated_vcf | File | ||
| docm_gatk_vcf | File | ||
| summary_hs_metrics | File[] | ||
| insert_size_metrics | File | ||
| per_base_hs_metrics | File[] | ||
| verify_bam_id_depth | File | ||
| insert_size_histogram | File | ||
| per_target_hs_metrics | File[] | ||
| verify_bam_id_metrics | File | ||
| mark_duplicates_metrics | File | ||
| alignment_summary_metrics | File | ||
| per_base_coverage_metrics | File[] | ||
| per_target_coverage_metrics | File[] | ||
| tumor_snv_bam_readcount_tsv | File | ||
| tumor_indel_bam_readcount_tsv | File |
Permalink:
https://w3id.org/cwl/view/git/54846feabbf008c1946db2a86d87252e0edd95b0/definitions/pipelines/tumor_only_exome.cwl
