pipelines_rnaseq_star_fusion.cwl

Documentation for rnaseq_star_fusion.cwl

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STAR-RNA-Seq alignment and transcript/gene abundance workflow

Name	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?

Name	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[]?

Name	CWL Run
sequence_to_trimmed_fastq	subworkflows/sequence_to_trimmed_fastq.cwl
strandedness_check	tools/strandedness_check.cwl
star_align_fusion	tools/star_align_fusion.cwl
star_fusion_detect	tools/star_fusion_detect.cwl
kallisto	tools/kallisto.cwl
transcript_to_gene	tools/transcript_to_gene.cwl
sort_bam	tools/samtools_sort.cwl
mark_dup	tools/mark_duplicates_and_sort.cwl
index_bam	tools/index_bam.cwl
stringtie	tools/stringtie.cwl
generate_qc_metrics	tools/generate_qc_metrics.cwl
bam_to_cram	tools/bam_to_cram.cwl
index_cram	tools/index_cram.cwl
cgpbigwig_bamcoverage	tools/bam_to_bigwig.cwl
agfusion	tools/agfusion.cwl