Workflow: gathered exome alignment and somatic variant detection for cle purpose
- Selected
- |
- 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 |
---|---|---|---|
mills | File | ||
docm_vcf | File | ||
omni_vcf | File | ||
vep_pick | |||
dbsnp_vcf | File | ||
reference | String | ||
output_dir | String | ||
known_indels | File | ||
somalier_vcf | File | ||
interval_list | File | ||
synonyms_file | File (Optional) | ||
vep_cache_dir | String (Optional) | ||
bait_intervals | File | ||
bqsr_intervals | String[] | ||
cle_vcf_filter | Boolean | ||
tumor_sequence | https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/types/sequence_data.yml#sequence_data[] | ||
hgvs_annotation | Boolean (Optional) | ||
normal_sequence | https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/types/sequence_data.yml#sequence_data[] | ||
tumor_cram_name | String (Optional) | ||
varscan_p_value | Float (Optional) | ||
normal_cram_name | String (Optional) | ||
target_intervals | File | ||
summary_intervals | https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/types/labelled_file.yml#labelled_file[] | ||
disclaimer_version | String | ||
per_base_intervals | https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/types/labelled_file.yml#labelled_file[] | ||
pindel_insert_size | Integer | ||
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) | ||
mutect_scatter_count | Integer | ||
per_target_intervals | https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/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/3b6d0475c80f5e452793a46a38ee188742b86595/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[] | ||
qc_minimum_mapping_quality | Integer (Optional) | ||
picard_metric_accumulation_level | String | ||
variants_to_table_genotype_fields | String[] |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
gatherer |
../tools/gatherer.cwl
(CommandLineTool)
|
||
somatic_exome |
somatic_exome_cle.cwl
(Workflow)
|
exome alignment and somatic variant detection for cle purpose |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
final_outputs | String[] |
Permalink:
https://w3id.org/cwl/view/git/3b6d0475c80f5e452793a46a38ee188742b86595/definitions/pipelines/somatic_exome_cle_gathered.cwl