pipelines_alignment_umi_molecular.cwl - genome/analysis-workflows GitHub Wiki
Documentation for alignment_umi_molecular.cwl
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Overview
umi molecular alignment fastq workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| 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 for FASTQs. For BAMs, this pipeline assumes that the RG information is already in the header. |
../types/sequence_data.yml#sequence_data[] |
|
| sample_name |
|
|
string |
|
| read_structure |
|
|
string[] |
|
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict', '.amb', '.ann', '.bwt', '.pac', '.sa'] |
| target_intervals |
|
|
File? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| aligned_cram |
|
|
File |
['.crai', '^.crai'] |
| adapter_histogram |
|
|
File[] |
|
| duplex_seq_metrics |
|
|
File[] |
|
Steps