tools_star_align_fusion.cwl

Documentation for star_align_fusion.cwl

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STAR: align reads to transcriptome

trinityctat/starfusion:1.10.1

Name	Description	Type
out_samtype		string[]
run_mode		string
fastq		File[]
fastq2		File[]
out_reads_unmapped		string
chim_segment_min		int
chim_junction_overhang_min		int
align_sjdb_overhang_min		int
align_mates_gapmax		int?
align_intron_max		int
chim_segment_read_gapmax		int
align_sjstitch_mismatch_nmax		int[]
outsam_strand_field		string
outsam_unmapped		string
outsam_attrrg_line	string(s): SAM/BAM read group line. The first word contains the read group identifier and must start with ID:, e.g. --outSAMattrRGline ID:xxx CN:yy DS:z z z. xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn	{'type': 'array', 'items': 'string'}
chim_multimap_nmax		int
chim_nonchim_scoredrop_min		int
peoverlap_nbases_min		int
peoverlap_mmp		float
chimout_junction_format		int
star_genome_dir	specifies path to the directory where the genome indices are stored	['string', 'Directory']
twopass_mode		string
reference_annotation	Annotated transcripts in GTF format; used as a source of splice junctions	File?
outfile_name_prefix		string
read_files_command		string?
outsam_attributes		string[]