subworkflows_molecular_alignment.cwl - genome/analysis-workflows GitHub Wiki
Documentation for molecular_alignment.cwl
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Overview
umi molecular alignment workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| bam |
|
|
File[] |
|
| sample_name |
|
|
string |
|
| read_structure |
|
|
string[] |
|
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] |
| target_intervals |
|
|
File? |
|
| min_reads |
|
|
int[] |
|
| max_read_error_rate |
|
|
float? |
|
| max_base_error_rate |
|
|
float? |
|
| min_base_quality |
|
|
int |
|
| max_no_call_fraction |
|
|
float |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| aligned_bam |
|
|
File |
['.bai', '^.bai'] |
| adapter_histogram |
|
|
File[] |
|
| duplex_seq_metrics |
|
|
File[] |
|
Steps