pipelines_alignment_exome.cwl - genome/analysis-workflows GitHub Wiki
Documentation for alignment_exome.cwl
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Overview
exome alignment with qc
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] |
| sequence |
sequence: sequencing data and readgroup information |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required. |
../types/sequence_data.yml#sequence_data[] |
|
| trimming |
|
|
['../types/trimming_options.yml#trimming_options', 'null'] |
|
| bqsr_known_sites |
|
One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis. |
File[] |
['.tbi'] |
| bqsr_intervals |
|
|
string[]? |
|
| bait_intervals |
|
|
File |
|
| final_name |
|
|
string? |
|
| target_intervals |
|
|
File |
|
| per_base_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| per_target_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| summary_intervals |
|
|
../types/labelled_file.yml#labelled_file[] |
|
| omni_vcf |
|
|
File |
['.tbi'] |
| picard_metric_accumulation_level |
|
|
string |
|
| qc_minimum_mapping_quality |
|
|
int? |
|
| qc_minimum_base_quality |
|
|
int? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| bam |
|
|
File |
['.bai', '^.bai'] |
| mark_duplicates_metrics |
|
|
File |
|
| insert_size_metrics |
|
|
File |
|
| insert_size_histogram |
|
|
File |
|
| alignment_summary_metrics |
|
|
File |
|
| hs_metrics |
|
|
File |
|
| per_target_coverage_metrics |
|
|
File[] |
|
| per_target_hs_metrics |
|
|
File[] |
|
| per_base_coverage_metrics |
|
|
File[] |
|
| per_base_hs_metrics |
|
|
File[] |
|
| summary_hs_metrics |
|
|
File[] |
|
| flagstats |
|
|
File |
|
| verify_bam_id_metrics |
|
|
File |
|
| verify_bam_id_depth |
|
|
File |
|
Steps