pipelines_bisulfite.cwl - genome/analysis-workflows GitHub Wiki
Documentation for bisulfite.cwl
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Overview
Bisulfite alignment and QC
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference_index |
|
|
string |
|
| reference_sizes |
|
|
File |
|
| instrument_data_bams |
|
|
File[] |
|
| read_group_id |
|
|
string[] |
|
| sample_name |
|
|
string |
|
| trimming_adapters |
|
|
File |
|
| trimming_adapter_trim_end |
|
|
string |
|
| trimming_adapter_min_overlap |
|
|
int |
|
| trimming_max_uncalled |
|
|
int |
|
| trimming_min_readlength |
|
|
int |
|
| QCannotation |
|
|
File |
|
| assay_non_cpg_sites |
|
Variable to determine if user wants to obtain obtain bed/bigwig files for non-CpG cytosines. Value - true or false |
{'type': 'enum', 'symbols': ['true', 'false']} |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| cram |
|
|
File |
['.crai', '^.crai'] |
| vcf |
|
|
File |
|
| cpgs |
|
|
File[] |
|
| cpg_bigwig |
|
|
File[] |
|
| gathered_directory |
|
|
Directory |
|
Steps