Workflow: exome alignment and tumor-only variant detection
Fetched 2023-01-05 02:43:27 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 |
|---|---|---|---|
| bams | File[] | ||
| mills | File | ||
| docm_vcf | File | ||
| omni_vcf | File | ||
| vep_pick | |||
| dbsnp_vcf | File | ||
| reference | String | ||
| readgroups | String[] | ||
| sample_name | String | ||
| known_indels | File | ||
| vep_assembly | String |
Used to explicitly define which version of the assembly to use; required if there are two or more in the same directory |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | String | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] (Optional) | ||
| varscan_p_value | Float (Optional) | ||
| target_intervals | File | ||
| custom_gnomad_vcf | File (Optional) | ||
| summary_intervals | https://w3id.org/cwl/view/git/c235dc6d623879a6c4f5fb307f545c9806eb2d23/definitions/types/labelled_file.yml#labelled_file[] | ||
| varscan_min_reads | Integer (Optional) | ||
| per_base_intervals | https://w3id.org/cwl/view/git/c235dc6d623879a6c4f5fb307f545c9806eb2d23/definitions/types/labelled_file.yml#labelled_file[] | ||
| vep_to_table_fields | String[] (Optional) | ||
| annotate_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/c235dc6d623879a6c4f5fb307f545c9806eb2d23/definitions/types/labelled_file.yml#labelled_file[] | ||
| varscan_min_coverage | Integer (Optional) | ||
| varscan_min_var_freq | Float (Optional) | ||
| varscan_strand_filter | Integer (Optional) | ||
| 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 |
exome_alignment.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/c235dc6d623879a6c4f5fb307f545c9806eb2d23/definitions/pipelines/exome.cwl
