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build_star_db

description: Runs STAR's build command to generate a STAR format reference for alignment
outputs: {'star_db': 'A gzipped TAR file containing the STAR reference files. Suitable as the star_db_tar_gz input to the alignment task.'}

Inputs

Required

_runtime (Any, required)
gtf (File, required): GTF format feature file
reference_fasta (File, required): The FASTA format reference file for the genome

Defaults

db_name (String, default="star_db"); description: Name for output in compressed, archived format. The suffix .tar.gz will be added.; common: true
genome_SA_index_n_bases (Int, default=14): length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1).
genome_SA_sparse_d (Int, default=1): suffix array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction.
genome_chr_bin_n_bits (Int, default=18): =log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).
genome_suffix_length_max (Int, default=-1): maximum length of the suffixes, has to be longer than read length. -1 = infinite.
memory_gb (Int, default=50): RAM to allocate for task, specified in GB
modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
ncpu (Int, default=8); description: Number of cores to allocate for task; common: true
sjdb_gtf_chr_prefix (String, default="-"); description: prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSEMBL annotations with UCSC genomes); common: true
sjdb_gtf_feature_exon (String, default="exon"): feature type in GTF file to be used as exons for building transcripts
sjdb_gtf_tag_exon_parant_transcript (String, default="transcript_id"): GTF attribute name for parent transcript ID
sjdb_gtf_tag_exon_parent_gene (String, default="gene_id"): GTF attribute name for parent gene ID
sjdb_gtf_tag_exon_parent_gene_name (String, default="gene_name"): GTF attribute name for parent gene name
sjdb_gtf_tag_exon_parent_gene_type (String, default="gene_type gene_biotype"): GTF attribute name for parent gene type
sjdb_overhang (Int, default=125); description: length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1). [STAR default]: 100. [WDL default]: 125.; common: true
use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true

Outputs

star_db (File)

alignment

description: Runs the STAR aligner on a set of RNA-Seq FASTQ files
external_help: https://github.com/alexdobin/STAR/blob/2.7.11b/doc/STARmanual.pdf
outputs: {'star_log': 'Summary mapping statistics after mapping job is complete. The statistics are calculated for each read (Single- or Paired-End) and then summed or averaged over all reads. Note that STAR counts a Paired-End read as one read. Most of the information is collected about the UNIQUE mappers. Each splicing is counted in the numbers of splices, which would correspond to summing the counts in SJ.out.tab. The mismatch/indel error rates are calculated on a per base basis, i.e. as total number of mismatches/indels in all unique mappers divided by the total number of mapped bases.', 'star_bam': 'STAR aligned BAM', 'star_junctions': 'File contains high confidence collapsed splice junctions in tab-delimited format. Note that STAR defines the junction start/end as intronic bases, while many other software define them as exonic bases. See meta.external_help for file specification.', 'star_chimeric_junctions': 'Tab delimited file containing chimeric reads and associated metadata. See meta.external_help for file specification.'}

Inputs

Required

_runtime (Any, required)
prefix (String, required): Prefix for the BAM and other STAR files. The extensions .Aligned.out.bam, .Log.final.out, .SJ.out.tab, and .Chimeric.out.junction will be added.
read_one_fastqs_gz (Array[File], required): An array of gzipped FASTQ files containing read one information
star_db_tar_gz (File, required): A gzipped TAR file containing the STAR reference files. The name of the root directory which was archived must match the archive's filename without the .tar.gz extension.

Optional

read_groups (String?): A string containing the read group information to output in the BAM file. If including multiple read group fields per-read group, they should be space delimited. Read groups should be comma separated, with a space on each side (i.e. ' , '). The ID field must come first for each read group and must be contained in the basename of a FASTQ file or pair of FASTQ files if Paired-End. Example: ID:rg1 PU:flowcell1.lane1 SM:sample1 PL:illumina LB:sample1_lib1 , ID:rg2 PU:flowcell1.lane2 SM:sample1 PL:illumina LB:sample1_lib1. These two read groups could be associated with the following four FASTQs: sample1.rg1_R1.fastq,sample1.rg2_R1.fastq and sample1.rg1_R2.fastq,sample1.rg2_R2.fastq

Defaults

align_ends_protrude (Pair[Int,String], default=(0, "ConcordantPair")); description: allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate. left: maximum number of protrusion bases allowed. right: see choices below.; choices: {'ConcordantPair': 'report alignments with non-zero protrusion as concordant pairs', 'DiscordantPair': 'report alignments with non-zero protrusion as discordant pairs'}
align_ends_type (String, default="Local"); description: type of read ends alignment; choices: {'Local': 'standard local alignment with soft-clipping allowed', 'EndToEnd': 'force end-to-end read alignment, do not soft-clip', 'Extend5pOfRead1': 'fully extend only the 5p of the read1, all other ends: local alignment', 'Extend5pOfReads12': 'fully extend only the 5p of the both read1 and read2, all other ends: local alignment'}
align_insertion_flush (String, default="None"); description: how to flush ambiguous insertion positions; choices: {'None': 'insertions are not flushed', 'Right': 'insertions are flushed to the right'}; common: true
align_intron_max (Int, default=500000); description: maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)winAnchorDistNbins. [STAR default]: 0. [WDL default]: 500000.; common*: true
align_intron_min (Int, default=21); description: minimum intron size: genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion; common: true
align_mates_gap_max (Int, default=1000000); description: maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)winAnchorDistNbins. [STAR default]: 0. [WDL default]: 1000000; common*: true
align_sj_overhang_min (Int, default=5); description: minimum overhang (i.e. block size) for spliced alignments; common: true
align_sj_stitch_mismatch_n_max (SpliceJunctionMotifs, default={"noncanonical_motifs": 0, "GT_AG_and_CT_AC_motif": -1, "GC_AG_and_CT_GC_motif": 0, "AT_AC_and_GT_AT_motif": 0}): maximum number of mismatches for stitching of the splice junctions (-1: no limit) for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif
align_sjdb_overhang_min (Int, default=1); description: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments. [STAR default]: 3. [WDL default]: 1.; common: true
align_soft_clip_at_reference_ends (String, default="Yes"); description: allow the soft-clipping of the alignments past the end of the chromosomes; choices: {'Yes': 'allow', 'No': 'prohibit, useful for compatibility with Cufflinks'}; common: true
align_spliced_mate_map_l_min (Int, default=0): minimum mapped length for a read mate that is spliced
align_spliced_mate_map_l_min_over_l_mate (Float, default=0.66): alignSplicedMateMapLmin normalized to mate length
align_transcripts_per_read_n_max (Int, default=10000): max number of different alignments per read to consider
align_transcripts_per_window_n_max (Int, default=100): max number of transcripts per window
align_windows_per_read_n_max (Int, default=10000): max number of windows per read
chim_filter (String, default="banGenomicN"); description: different filters for chimeric alignments; choices: {'None': 'no filtering', 'banGenomicN': 'Ns are not allowed in the genome sequence around the chimeric junction'}
chim_junction_overhang_min (Int, default=20); description: minimum overhang for a chimeric junction; common: true
chim_main_segment_multi_n_max (Int, default=10); description: maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments.; common: true
chim_multimap_n_max (Int, default=0); description: maximum number of chimeric multi-alignments. 0: use the old scheme for chimeric detection which only considered unique alignments; common: true
chim_multimap_score_range (Int, default=1): the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax > 1.
chim_nonchim_score_drop_min (Int, default=20): to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value
chim_out_junction_format (String, default="plain"); description: formatting type for the Chimeric.out.junction file; choices: {'plain': 'no comment lines/headers', 'comments': 'comment lines at the end of the file: command line and Nreads: total, unique/multi-mapping'}; common: true
chim_out_type (String, default="WithinBAM HardClip"); description: type of chimeric output; choices: {'Junctions': 'Chimeric.out.junction', 'WithinBAM_HardClip': 'output into main aligned BAM files (Aligned..bam). Hard-clipping in the CIGAR for supplemental chimeric alignments.', 'WithinBAM_SoftClip': 'output into main aligned BAM files (Aligned..bam). Soft-clipping in the CIGAR for supplemental chimeric alignments.'}; tool_default: Junctions; common: true
chim_score_drop_max (Int, default=20); description: max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length; common: true
chim_score_junction_nonGTAG (Int, default=-1): penalty for a non-GT/AG chimeric junction
chim_score_min (Int, default=0); description: minimum total (summed) score of the chimeric segments; common: true
chim_score_separation (Int, default=10): minimum difference (separation) between the best chimeric score and the next one
chim_segment_min (Int, default=10); description: minimum length of chimeric segment length, if ==0, no chimeric output; tool_default: 0; common: true
chim_segment_read_gap_max (Int, default=0); description: maximum gap in the read sequence between chimeric segments; common: true
clip_3p_adapter_mmp (Pair[Float,Float], default=(0.1, 0.1)): max proportion of mismatches for 3p adapter clipping for each mate. left applies to read one and right applies to read two.
clip_3p_adapter_seq (Pair[String,String], default=("None", "None")); description: adapter sequences to clip from 3p of each mate. left applies to read one and right applies to read two.; choices: {'None': 'No 3p adapter trimming will be performed', 'sequence': 'A nucleotide sequence string of any length, matching the regex /[ATCG]+/', 'polyA': 'polyA sequence with the length equal to read length'}; common: true
clip_3p_after_adapter_n_bases (Pair[Int,Int], default=(0, 0)): number of bases to clip from 3p of each mate after the adapter clipping. left applies to read one and right applies to read two.
clip_3p_n_bases (Pair[Int,Int], default=(0, 0)): number of bases to clip from 3p of each mate. left applies to read one and right applies to read two.
clip_5p_n_bases (Pair[Int,Int], default=(0, 0)): number of bases to clip from 5p of each mate. left applies to read one and right applies to read two.
clip_adapter_type (String, default="Hamming"); description: adapter clipping type; choices: {'Hamming': 'adapter clipping based on Hamming distance, with the number of mismatches controlled by --clip5pAdapterMMp', 'CellRanger4': '5p and 3p adapter clipping similar to CellRanger4. Utilizes Opal package by Martin Šošić: https://github.com/Martinsos/opal', 'None': 'no adapter clipping, all other clip* parameters are disregarded'}
limit_out_sj_collapsed (Int, default=1000000): max number of collapsed junctions
limit_out_sj_one_read (Int, default=1000): max number of junctions for one read (including all multi-mappers)
limit_sjdb_insert_n_sj (Int, default=1000000): maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run
modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
ncpu (Int, default=8); description: Number of cores to allocate for task; common: true
out_QS_conversion_add (Int, default=0): add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31)
out_filter_intron_motifs (String, default="None"); description: filter alignment using their motifs; choices: {'None': 'no filtering', 'RemoveNoncanonical': 'filter out alignments that contain non-canonical junctions', 'RemoveNoncanonicalUnannotated': 'filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept.'}; common: true
out_filter_intron_strands (String, default="RemoveInconsistentStrands"); description: filter alignments; choices: {'None': 'no filtering', 'RemoveInconsistentStrands': 'remove alignments that have junctions with inconsistent strands'}; common: true
out_filter_match_n_min (Int, default=0); description: alignment will be output only if the number of matched bases is higher than or equal to this value; common: true
out_filter_match_n_min_over_l_read (Float, default=0.66): same as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for Paired-End reads)
out_filter_mismatch_n_max (Int, default=10); description: alignment will be output only if it has no more mismatches than this value; common: true
out_filter_mismatch_n_over_l_max (Float, default=0.3): alignment will be output only if its ratio of mismatches to mapped length is less than or equal to this value
out_filter_mismatch_n_over_read_l_max (Float, default=1.0): alignment will be output only if its ratio of mismatches to read length is less than or equal to this value
out_filter_multimap_n_max (Int, default=10); description: maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value. Otherwise no alignments will be output, and the read will be counted as 'mapped to too many loci' in the Log.final.out. [STAR default]: 10. [WDL default]: 20.; common: true
out_filter_multimap_score_range (Int, default=1): the score range below the maximum score for multimapping alignments
out_filter_score_min (Int, default=0); description: alignment will be output only if its score is higher than or equal to this value; common: true
out_filter_score_min_over_l_read (Float, default=0.66): same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for Paired-End reads)
out_filter_type (String, default="Normal"); description: type of filtering; choices: {'Normal': 'standard filtering using only current alignment', 'BySJout': 'keep only those reads that contain junctions that passed filtering into SJ.out.tab'}; common: true
out_sam_attr_IH_start (Int, default=1): start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie.
out_sam_attributes (String, default="NH HI AS nM NM MD XS"); description: a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order. [STAR defaults]: NH HI AS nM. [WDL default]: NH HI AS nM NM MD XS.; choices: {'NH': 'number of loci the reads maps to: =1 for unique mappers, >1 for multimappers. Standard SAM tag.', 'HI': 'multiple alignment index, starts with --outSAMattrIHstart (=1 by default). Standard SAM tag.', 'AS': 'local alignment score, +1/-1 for matches/mismateches, score penalties for indels and gaps. For PE reads, total score for two mates. Standard SAM tag.', 'nM': 'number of mismatches. For PE reads, sum over two mates.', 'NM': 'edit distance to the reference (number of mismatched + inserted + deleted bases) for each mate. Standard SAM tag.', 'MD': 'string encoding mismatched and deleted reference bases (see standard SAM specifications). Standard SAM tag.', 'jM': 'intron motifs for all junctions (i.e. N in CIGAR): 0: non-canonical; 1: GT/AG, 2: CT/AC, 3: GC/AG, 4: CT/GC, 5: AT/AC, 6: GT/AT. If splice junctions database is used, and a junction is annotated, 20 is added to its motif value.', 'jI': 'start and end of introns for all junctions (1-based).', 'XS': 'alignment strand according to --outSAMstrandField.', 'MC': "mate's CIGAR string. Standard SAM tag.", 'ch': 'marks all segments of all chimeric alignments for --chimOutType WithinBAM output.', 'cN': "number of bases clipped from the read ends: 5' and 3'"}; common*: true
out_sam_flag_AND (Int, default=65535): 0-65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise.
out_sam_flag_OR (Int, default=0): 0-65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise.
out_sam_mapq_unique (Int, default=254): 0-255: the MAPQ value for unique mappers. Please note the STAR default (255) produces errors downstream, as a MAPQ value of 255 is reserved to indicate a missing value. The default of this task is 254, which is the highest valid MAPQ value, and possibly what the author of STAR intended. [STAR default]: 255. [WDL default]: 254.
out_sam_order (String, default="Paired"); description: type of sorting for the SAM output; choices: {'Paired': 'one mate after the other for all paired alignments', 'PairedKeepInputOrder': 'one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files'}
out_sam_read_id (String, default="Standard"); description: read ID record type; choices: {'Standard': 'first word (until space) from the FASTx read ID line, removing /1,/2 from the end', 'Number': 'read number (index) in the FASTx file'}
out_sam_strand_field (String, default="intronMotif"); description: Cufflinks-like strand field flag; choices: {'None': 'not used', 'intronMotif': 'strand derived from the intron motif. This option changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out.'}; common: true
out_sam_tlen (String, default="left_plus"); description: calculation method for the TLEN field in the SAM/BAM files; choices: {'left_plus': 'leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate', 'left_any': 'leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from left_plus for overlapping mates with protruding ends'}
out_sam_unmapped (String, default="Within"); description: output of unmapped reads in the SAM format.; choices: {'None': 'no output [STAR default]', 'Within': 'output unmapped reads within the main SAM file (i.e. Aligned.out.sam) [WDL default]'}
out_sj_filter_count_total_min (SpliceJunctionMotifs, default={"noncanonical_motifs": 3, "GT_AG_and_CT_AC_motif": 1, "GC_AG_and_CT_GC_motif": 1, "AT_AC_and_GT_AT_motif": 1}): minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif. Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied. Does not apply to annotated junctions.
out_sj_filter_count_unique_min (SpliceJunctionMotifs, default={"noncanonical_motifs": 3, "GT_AG_and_CT_AC_motif": 1, "GC_AG_and_CT_GC_motif": 1, "AT_AC_and_GT_AT_motif": 1}): minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif. Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied. Does not apply to annotated junctions.
out_sj_filter_dist_to_other_sj_min (SpliceJunctionMotifs, default={"noncanonical_motifs": 10, "GT_AG_and_CT_AC_motif": 0, "GC_AG_and_CT_GC_motif": 5, "AT_AC_and_GT_AT_motif": 10}): minimum allowed distance to other junctions' donor/acceptor for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. Does not apply to annotated junctions.
out_sj_filter_intron_max_vs_read_n (Array[Int], default=[50000, 100000, 200000]): maximum gap allowed for junctions supported by 1,2,3,,,N reads. i.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000b. by >=4 reads any gap <=alignIntronMax. Does not apply to annotated junctions.
out_sj_filter_overhang_min (SpliceJunctionMotifs, default={"noncanonical_motifs": 30, "GT_AG_and_CT_AC_motif": 12, "GC_AG_and_CT_GC_motif": 12, "AT_AC_and_GT_AT_motif": 12}): minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif. Does not apply to annotated junctions.
out_sj_filter_reads (String, default="All"); description: which reads to consider for collapsed splice junctions output; choices: {'All': 'all reads, unique- and multi-mappers', 'Unique': 'uniquely mapping reads only'}; common: true
pe_overlap_mmp (Float, default=0.01): maximum proportion of mismatched bases in the overlap area
pe_overlap_n_bases_min (Int, default=0): minimum number of overlap bases to trigger mates merging and realignment. Specify >0 value to switch on the 'merging of overlapping mates' algorithm.
read_map_number (Int, default=-1); description: number of reads to map from the beginning of the file. -1 to map all reads; common: true
read_name_separator (String, default="/"): character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed)
read_quality_score_base (Int, default=33): number to be subtracted from the ASCII code to get Phred quality score
read_two_fastqs_gz (Array[File], default=[]); description: An array of gzipped FASTQ files containing read two information; common: true
run_rng_seed (Int, default=777); description: random number generator seed; common: true
score_del_base (Int, default=-2): deletion extension penalty per base (in addition to scoreDelOpen)
score_del_open (Int, default=-2): deletion open penalty
score_gap (Int, default=0): splice junction penalty (independent on intron motif)
score_gap_ATAC (Int, default=-8): AT/AC and GT/AT junction penalty (in addition to scoreGap)
score_gap_GCAG (Int, default=-4): GC/AG and CT/GC junction penalty (in addition to scoreGap)
score_gap_noncanon (Int, default=-8): non-canonical junction penalty (in addition to scoreGap)
score_genomic_length_log2_scale (Float, default=-0.25): extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength)
score_ins_base (Int, default=-2): insertion extension penalty per base (in addition to scoreInsOpen)
score_ins_open (Int, default=-2): insertion open penalty
score_stitch_sj_shift (Int, default=1): maximum score reduction while searching for SJ boundaries in the stitching step
seed_map_min (Int, default=5): min length of seeds to be mapped
seed_multimap_n_max (Int, default=10000): only pieces that map fewer than this value are utilized in the stitching procedure
seed_none_loci_per_window (Int, default=10): max number of one seed loci per window
seed_per_read_n_max (Int, default=1000): max number of seeds per read
seed_per_window_n_max (Int, default=50): max number of seeds per window
seed_search_l_max (Int, default=0): defines the maximum length of the seeds, if =0 seed length is not limited
seed_search_start_l_max (Int, default=50): defines the search start point through the read - the read is split into pieces no longer than this value
seed_search_start_l_max_over_l_read (Float, default=1.0): seedSearchStartLmax normalized to read length (sum of mates' lengths for Paired-End reads)
seed_split_min (Int, default=12): min length of the seed sequences split by Ns or mate gap
sjdb_score (Int, default=2); description: extra alignment score for alignments that cross database junctions; common: true
twopass1_reads_n (Int, default=-1); description: number of reads to process for the 1st step. Use default (-1) to map all reads in the first step; common: true
twopass_mode (String, default="Basic"); description: 2-pass mapping mode; choices: {'None': '1-pass mapping [STAR default]', 'Basic': 'basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly [WDL default]'}; common: true
use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true
win_anchor_dist_n_bins (Int, default=9): max number of bins between two anchors that allows aggregation of anchors into one window
win_anchor_multimap_n_max (Int, default=50): max number of loci anchors are allowed to map to
win_bin_n_bits (Int, default=16): =log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins
win_flank_n_bins (Int, default=4): =log2(winFlank), where winFlank is the size of the left and right flanking regions for each window

Outputs

star_log (File)
star_bam (File)
star_junctions (File)
star_chimeric_junctions (File?)