pipelines_rnaseq.cwl - genome/analysis-workflows GitHub Wiki
Documentation for rnaseq.cwl
This page is auto-generated. Do not edit.
Overview
RNA-Seq alignment and transcript/gene abundance workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| reference_index |
|
|
File |
['.1.ht2', '.2.ht2', '.3.ht2', '.4.ht2', '.5.ht2', '.6.ht2', '.7.ht2', '.8.ht2'] |
| reference_annotation |
|
|
File |
|
| rna_sequence |
|
|
../types/sequence_data.yml#sequence_data[] |
|
| read_group_id |
|
|
string[] |
|
| read_group_fields |
|
|
{'type': 'array', 'items': {'type': 'array', 'items': '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 |
|
| kallisto_index |
|
|
File |
|
| gene_transcript_lookup_table |
|
|
File |
|
| strand |
|
|
['null', {'type': 'enum', 'symbols': ['first', 'second', 'unstranded']}] |
|
| refFlat |
|
|
File |
|
| ribosomal_intervals |
|
|
File? |
|
| species |
|
the species being analyzed, such as homo_sapiens or mus_musculus |
string |
|
| assembly |
|
the assembly used, such as GRCh37/38, GRCm37/38 |
string |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| final_bam |
|
|
File |
['.bai'] |
| stringtie_transcript_gtf |
|
|
File |
|
| stringtie_gene_expression_tsv |
|
|
File |
|
| transcript_abundance_tsv |
|
|
File |
|
| transcript_abundance_h5 |
|
|
File |
|
| gene_abundance |
|
|
File |
|
| metrics |
|
|
File |
|
| chart |
|
|
File? |
|
| fusion_evidence |
|
|
File |
|
| bamcoverage_bigwig |
|
|
File |
|
Steps