Workflow: gather AML trio outputs
Fetched 2023-01-04 17:56:37 GMT
Verified with cwltool version 3.1.20221201130942
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- Default Values
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- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| docm_vcf | File | ||
| omni_vcf | File | ||
| vep_pick | |||
| intervals | 7255a22cdc5df0e42632a8cc2712500d[] | ||
| reference | String | ||
| output_dir | String | ||
| tumor_name | String (Optional) | ||
| normal_name | String (Optional) | ||
| somalier_vcf | File | ||
| followup_name | String (Optional) | ||
| gvcf_gq_bands | String[] | ||
| interval_list | File | ||
| scatter_count | Integer |
scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs |
|
| synonyms_file | File (Optional) | ||
| vep_cache_dir | Directory | ||
| bait_intervals | File | ||
| bqsr_intervals | String[] | ||
| cle_vcf_filter | Boolean | ||
| tumor_sequence | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/sequence_data.yml#sequence_data[] | tumor_sequence: MT sequencing data and readgroup information |
tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| disclaimer_text | String (Optional) | ||
| normal_sequence | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/sequence_data.yml#sequence_data[] | normal_sequence: WT sequencing data and readgroup information |
normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
| varscan_p_value | Float (Optional) | ||
| bqsr_known_sites | File[] |
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
|
| target_intervals | File | ||
| followup_sequence | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/sequence_data.yml#sequence_data[] | ||
| summary_intervals | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/labelled_file.yml#labelled_file[] | ||
| tumor_sample_name | String | ||
| disclaimer_version | String | ||
| normal_sample_name | String | ||
| per_base_intervals | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/labelled_file.yml#labelled_file[] | ||
| pindel_insert_size | Integer | ||
| pindel_region_file | File | ||
| germline_tsv_prefix | String (Optional) | ||
| 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_docm_variants | Boolean (Optional) | ||
| filter_minimum_depth | Integer (Optional) | ||
| germline_coding_only | Boolean (Optional) | ||
| per_target_intervals | https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/labelled_file.yml#labelled_file[] | ||
| strelka_cpu_reserved | Integer (Optional) | ||
| 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/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/types/vep_custom_annotation.yml#vep_custom_annotation[] |
custom type, check types directory for input format |
|
| qc_minimum_base_quality | Integer (Optional) | ||
| varscan_max_normal_freq | Float (Optional) | ||
| variants_to_table_fields | String[] | ||
| emit_reference_confidence | |||
| qc_minimum_mapping_quality | Integer (Optional) | ||
| variant_reporting_intervals | File | ||
| germline_vep_to_table_fields | String[] | ||
| picard_metric_accumulation_level | String | ||
| germline_variants_to_table_fields | String[] | ||
| variants_to_table_genotype_fields | String[] | ||
| germline_variants_to_table_genotype_fields | String[] |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| aml_trio |
aml_trio_cle.cwl
(Workflow)
|
Replace legacy AML Trio Assay | |
| gatherer |
../tools/gatherer.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| final_outputs | String[] |
https://w3id.org/cwl/view/git/77ec4f26eb14ed82481828bd9f6ef659cfd8b40f/definitions/pipelines/aml_trio_cle_gathered.cwl
