tools_star_align_fusion.cwl

Documentation for star_align_fusion.cwl

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Overview

STAR: align reads to transcriptome

Docker Requirement

trinityctat/starfusion:1.10.1

Inputs

Name	Label	Description	Type	Secondary Files
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[]

Outputs

Name	Label	Description	Type	Secondary Files
aligned_bam			File
log_final			File
log			File
log_progress			File
splice_junction_out			File
chim_junc			File