pipelines_rnaseq_star_fusion.cwl - genome/analysis-workflows GitHub Wiki
Documentation for rnaseq_star_fusion.cwl
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Overview
STAR-RNA-Seq alignment and transcript/gene abundance workflow
Inputs
| Name |
Label |
Description |
Type |
Secondary Files |
| unaligned |
|
Raw data from rna sequencing; this custom type holds both the data file(s) and readgroup information. Data file(s) may be either a bam file, or paired fastqs. Readgroup information should be given as a series of key:value pairs, each separated by a space. This means that spaces within a value must be double quoted. The first key must be ID; consult the read group description in the header section of the SAM file specification for other, optional keys. Below is an example of an element of the input array: readgroup: "ID:xxx PU:xxx SM:xxx LB:xxx PL:ILLUMINA CN:WUGSC" sequence: fastq1: class: File path: /path/to/reads1.fastq fastq2: class: File path: /path/to/reads2.fastq OR bam: class: File path: /path/to/reads.bam |
../types/sequence_data.yml#sequence_data[] |
|
| star_genome_dir |
|
|
['string', 'Directory'] |
|
| star_fusion_genome_dir |
|
|
['string', 'Directory'] |
|
| cdna_fasta |
|
|
File |
|
| reference |
|
|
['string', 'File'] |
['.fai', '^.dict'] |
| reference_annotation |
|
|
File |
|
| 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 |
|
| sample_name |
|
|
string |
|
| unzip_fastqs |
|
|
boolean? |
|
| examine_coding_effect |
|
|
boolean? |
|
| fusioninspector_mode |
|
|
['null', {'type': 'enum', 'symbols': ['inspect', 'validate']}] |
|
| agfusion_database |
|
|
File |
|
| agfusion_annotate_noncanonical |
|
|
boolean? |
|
Outputs
| Name |
Label |
Description |
Type |
Secondary Files |
| cram |
|
|
File |
['.crai', '^.crai'] |
| star_fusion_out |
|
|
File |
|
| star_junction_out |
|
|
File |
|
| star_fusion_log |
|
|
File |
|
| star_fusion_predict |
|
|
File |
|
| star_fusion_abridge |
|
|
File |
|
| 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 |
|
| strand_info |
|
|
File[] |
|
| bamcoverage_bigwig |
|
|
File |
|
| final_bam |
|
|
File |
['.bai'] |
| annotated_fusion_predictions |
|
|
Directory |
|
| coding_region_effects |
|
|
File? |
|
| fusioninspector_evidence |
|
|
File[]? |
|
Steps