argument_groups:
- name: Run Parameters
  arguments:
  - name: --runRNGseed
    type: integer
    description: random number generator seed.
    example: 777
- name: Genome Parameters
  arguments:
  - name: --genomeDir
    type: file
    description: path to the directory where genome files are stored (for --runMode
      alignReads) or will be generated (for --runMode generateGenome)
    example: ./GenomeDir/
    required: yes
  - name: --genomeLoad
    type: string
    description: |-
      mode of shared memory usage for the genome files. Only used with --runMode alignReads.

      - LoadAndKeep     ... load genome into shared and keep it in memory after run
      - LoadAndRemove   ... load genome into shared but remove it after run
      - LoadAndExit     ... load genome into shared memory and exit, keeping the genome in memory for future runs
      - Remove          ... do not map anything, just remove loaded genome from memory
      - NoSharedMemory  ... do not use shared memory, each job will have its own private copy of the genome
    example: NoSharedMemory
  - name: --genomeFastaFiles
    type: file
    description: |-
      path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped.

      Required for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins).
    multiple: yes
    multiple_sep: ;
  - name: --genomeFileSizes
    type: integer
    description: genome files exact sizes in bytes. Typically, this should not be
      defined by the user.
    example: 0
    multiple: yes
    multiple_sep: ;
  - name: --genomeTransformOutput
    type: string
    description: |-
      which output to transform back to original genome

      - SAM     ... SAM/BAM alignments
      - SJ      ... splice junctions (SJ.out.tab)
      - Quant   ... quantifications (from --quantMode option)
      - None    ... no transformation of the output
    multiple: yes
    multiple_sep: ;
  - name: --genomeChrSetMitochondrial
    type: string
    description: names of the mitochondrial chromosomes. Presently only used for STARsolo
      statistics output/
    example:
    - chrM
    - M
    - MT
    multiple: yes
    multiple_sep: ;
- name: Splice Junctions Database
  arguments:
  - name: --sjdbFileChrStartEnd
    type: string
    description: path to the files with genomic coordinates (chr <tab> start <tab>
      end <tab> strand) for the splice junction introns. Multiple files can be supplied
      and will be concatenated.
    multiple: yes
    multiple_sep: ;
  - name: --sjdbGTFfile
    type: file
    description: path to the GTF file with annotations
  - name: --sjdbGTFchrPrefix
    type: string
    description: prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL
      annotations with UCSC genomes)
  - name: --sjdbGTFfeatureExon
    type: string
    description: feature type in GTF file to be used as exons for building transcripts
    example: exon
  - name: --sjdbGTFtagExonParentTranscript
    type: string
    description: GTF attribute name for parent transcript ID (default "transcript_id"
      works for GTF files)
    example: transcript_id
  - name: --sjdbGTFtagExonParentGene
    type: string
    description: GTF attribute name for parent gene ID (default "gene_id" works for
      GTF files)
    example: gene_id
  - name: --sjdbGTFtagExonParentGeneName
    type: string
    description: GTF attribute name for parent gene name
    example: gene_name
    multiple: yes
    multiple_sep: ;
  - name: --sjdbGTFtagExonParentGeneType
    type: string
    description: GTF attribute name for parent gene type
    example:
    - gene_type
    - gene_biotype
    multiple: yes
    multiple_sep: ;
  - name: --sjdbOverhang
    type: integer
    description: length of the donor/acceptor sequence on each side of the junctions,
      ideally = (mate_length - 1)
    example: 100
  - name: --sjdbScore
    type: integer
    description: extra alignment score for alignments that cross database junctions
    example: 2
  - name: --sjdbInsertSave
    type: string
    description: |-
      which files to save when sjdb junctions are inserted on the fly at the mapping step

      - Basic ... only small junction / transcript files
      - All   ... all files including big Genome, SA and SAindex - this will create a complete genome directory
    example: Basic
- name: Variation parameters
  arguments:
  - name: --varVCFfile
    type: string
    description: path to the VCF file that contains variation data. The 10th column
      should contain the genotype information, e.g. 0/1
- name: Read Parameters
  arguments:
  - name: --readFilesType
    type: string
    description: |-
      format of input read files

      - Fastx       ... FASTA or FASTQ
      - SAM SE      ... SAM or BAM single-end reads; for BAM use --readFilesCommand samtools view
      - SAM PE      ... SAM or BAM paired-end reads; for BAM use --readFilesCommand samtools view
    example: Fastx
  - name: --readFilesSAMattrKeep
    type: string
    description: |-
      for --readFilesType SAM SE/PE, which SAM tags to keep in the output BAM, e.g.: --readFilesSAMtagsKeep RG PL

      - All     ... keep all tags
      - None    ... do not keep any tags
    example: All
    multiple: yes
    multiple_sep: ;
  - name: --readFilesManifest
    type: file
    description: |-
      path to the "manifest" file with the names of read files. The manifest file should contain 3 tab-separated columns:

      paired-end reads: read1_file_name $tab$ read2_file_name $tab$ read_group_line.
      single-end reads: read1_file_name $tab$ -               $tab$ read_group_line.
      Spaces, but not tabs are allowed in file names.
      If read_group_line does not start with ID:, it can only contain one ID field, and ID: will be added to it.
      If read_group_line starts with ID:, it can contain several fields separated by $tab$, and all fields will be be copied verbatim into SAM @RG header line.
  - name: --readFilesPrefix
    type: string
    description: prefix for the read files names, i.e. it will be added in front of
      the strings in --readFilesIn
  - name: --readFilesCommand
    type: string
    description: |-
      command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout

      For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc.
    multiple: yes
    multiple_sep: ;
  - name: --readMapNumber
    type: integer
    description: |-
      number of reads to map from the beginning of the file

      -1: map all reads
    example: -1
  - name: --readMatesLengthsIn
    type: string
    description: Equal/NotEqual - lengths of names,sequences,qualities for both mates
      are the same  / not the same. NotEqual is safe in all situations.
    example: NotEqual
  - name: --readNameSeparator
    type: string
    description: character(s) separating the part of the read names that will be trimmed
      in output (read name after space is always trimmed)
    example: /
    multiple: yes
    multiple_sep: ;
  - name: --readQualityScoreBase
    type: integer
    description: number to be subtracted from the ASCII code to get Phred quality
      score
    example: 33
- name: Read Clipping
  arguments:
  - name: --clipAdapterType
    type: string
    description: |-
      adapter clipping type

      - 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 Sosic: https://github.com/Martinsos/opal
      - None ... no adapter clipping, all other clip* parameters are disregarded
    example: Hamming
  - name: --clip3pNbases
    type: integer
    description: number(s) of bases to clip from 3p of each mate. If one value is
      given, it will be assumed the same for both mates.
    example: 0
    multiple: yes
    multiple_sep: ;
  - name: --clip3pAdapterSeq
    type: string
    description: |-
      adapter sequences to clip from 3p of each mate.  If one value is given, it will be assumed the same for both mates.

      - polyA ... polyA sequence with the length equal to read length
    multiple: yes
    multiple_sep: ;
  - name: --clip3pAdapterMMp
    type: double
    description: max proportion of mismatches for 3p adapter clipping for each mate.  If
      one value is given, it will be assumed the same for both mates.
    example: 0.1
    multiple: yes
    multiple_sep: ;
  - name: --clip3pAfterAdapterNbases
    type: integer
    description: number of bases to clip from 3p of each mate after the adapter clipping.
      If one value is given, it will be assumed the same for both mates.
    example: 0
    multiple: yes
    multiple_sep: ;
  - name: --clip5pNbases
    type: integer
    description: number(s) of bases to clip from 5p of each mate. If one value is
      given, it will be assumed the same for both mates.
    example: 0
    multiple: yes
    multiple_sep: ;
- name: Limits
  arguments:
  - name: --limitGenomeGenerateRAM
    type: long
    description: maximum available RAM (bytes) for genome generation
    example: '31000000000'
  - name: --limitIObufferSize
    type: long
    description: max available buffers size (bytes) for input/output, per thread
    example:
    - 30000000
    - 50000000
    multiple: yes
    multiple_sep: ;
  - name: --limitOutSAMoneReadBytes
    type: long
    description: 'max size of the SAM record (bytes) for one read. Recommended value:
      >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax'
    example: 100000
  - name: --limitOutSJoneRead
    type: integer
    description: max number of junctions for one read (including all multi-mappers)
    example: 1000
  - name: --limitOutSJcollapsed
    type: integer
    description: max number of collapsed junctions
    example: 1000000
  - name: --limitBAMsortRAM
    type: long
    description: maximum available RAM (bytes) for sorting BAM. If =0, it will be
      set to the genome index size. 0 value can only be used with --genomeLoad NoSharedMemory
      option.
    example: 0
  - name: --limitSjdbInsertNsj
    type: integer
    description: maximum number of junctions 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
    example: 1000000
  - name: --limitNreadsSoft
    type: integer
    description: soft limit on the number of reads
    example: -1
- name: 'Output: general'
  arguments:
  - name: --outTmpKeep
    type: string
    description: |-
      whether to keep the temporary files after STAR runs is finished

      - None ... remove all temporary files
      - All ... keep all files
  - name: --outStd
    type: string
    description: |-
      which output will be directed to stdout (standard out)

      - Log                    ... log messages
      - SAM                    ... alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out
      - BAM_Unsorted           ... alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted
      - BAM_SortedByCoordinate ... alignments in BAM format, sorted by coordinate. Requires --outSAMtype BAM SortedByCoordinate
      - BAM_Quant              ... alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM
    example: Log
  - name: --outReadsUnmapped
    type: string
    description: |-
      output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s).

      - None    ... no output
      - Fastx   ... output in separate fasta/fastq files, Unmapped.out.mate1/2
  - name: --outQSconversionAdd
    type: integer
    description: add this number to the quality score (e.g. to convert from Illumina
      to Sanger, use -31)
    example: 0
  - name: --outMultimapperOrder
    type: string
    description: |-
      order of multimapping alignments in the output files

      - Old_2.4             ... quasi-random order used before 2.5.0
      - Random              ... random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases.
    example: Old_2.4
- name: 'Output: SAM and BAM'
  arguments:
  - name: --outSAMtype
    type: string
    description: |-
      type of SAM/BAM output

      1st word:
      - BAM  ... output BAM without sorting
      - SAM  ... output SAM without sorting
      - None ... no SAM/BAM output
      2nd, 3rd:
      - Unsorted           ... standard unsorted
      - SortedByCoordinate ... sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limitBAMsortRAM.
    example: SAM
    multiple: yes
    multiple_sep: ;
  - name: --outSAMmode
    type: string
    description: |-
      mode of SAM output

      - None ... no SAM output
      - Full ... full SAM output
      - NoQS ... full SAM but without quality scores
    example: Full
  - name: --outSAMstrandField
    type: string
    description: |-
      Cufflinks-like strand field flag

      - 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.
  - name: --outSAMattributes
    type: string
    description: |-
      a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order.

      ***Presets:
      - None        ... no attributes
      - Standard    ... NH HI AS nM
      - All         ... NH HI AS nM NM MD jM jI MC ch
      ***Alignment:
      - 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. Stadnard 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 segment of all chimeric alingments for --chimOutType WithinBAM output.
      - cN          ... number of bases clipped from the read ends: 5' and 3'
      ***Variation:
      - vA          ... variant allele
      - vG          ... genomic coordinate of the variant overlapped by the read.
      - vW          ... 1 - alignment passes WASP filtering; 2,3,4,5,6,7 - alignment does not pass WASP filtering. Requires --waspOutputMode SAMtag.
      - ha          ... haplotype (1/2) when mapping to the diploid genome. Requires genome generated with --genomeTransformType Diploid .
      ***STARsolo:
      - CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing.
      - GX GN       ... gene ID and gene name for unique-gene reads.
      - gx gn       ... gene IDs and gene names for unique- and multi-gene reads.
      - CB UB       ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate.
      - sM          ... assessment of CB and UMI.
      - sS          ... sequence of the entire barcode (CB,UMI,adapter).
      - sQ          ... quality of the entire barcode.
      - sF          ... type of feature overlap and number of features for each alignment
      ***Unsupported/undocumented:
      - rB          ... alignment block read/genomic coordinates.
      - vR          ... read coordinate of the variant.
    example: Standard
    multiple: yes
    multiple_sep: ;
  - name: --outSAMattrIHstart
    type: integer
    description: start value for the IH attribute. 0 may be required by some downstream
      software, such as Cufflinks or StringTie.
    example: 1
  - name: --outSAMunmapped
    type: string
    description: |-
      output of unmapped reads in the SAM format

      1st word:
      - None   ... no output
      - Within ... output unmapped reads within the main SAM file (i.e. Aligned.out.sam)
      2nd word:
      - KeepPairs ... record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects multi-mapping reads.
    multiple: yes
    multiple_sep: ;
  - name: --outSAMorder
    type: string
    description: |-
      type of sorting for the SAM output

      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
    example: Paired
  - name: --outSAMprimaryFlag
    type: string
    description: |-
      which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG

      - OneBestScore ... only one alignment with the best score is primary
      - AllBestScore ... all alignments with the best score are primary
    example: OneBestScore
  - name: --outSAMreadID
    type: string
    description: |-
      read ID record type

      - 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
    example: Standard
  - name: --outSAMmapqUnique
    type: integer
    description: '0 to 255: the MAPQ value for unique mappers'
    example: 255
  - name: --outSAMflagOR
    type: integer
    description: '0 to 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.'
    example: 0
  - name: --outSAMflagAND
    type: integer
    description: '0 to 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.'
    example: 65535
  - name: --outSAMattrRGline
    type: string
    description: |-
      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. Commas have to be surrounded by spaces, e.g.
      --outSAMattrRGline ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy
    multiple: yes
    multiple_sep: ;
  - name: --outSAMheaderHD
    type: string
    description: '@HD (header) line of the SAM header'
    multiple: yes
    multiple_sep: ;
  - name: --outSAMheaderPG
    type: string
    description: extra @PG (software) line of the SAM header (in addition to STAR)
    multiple: yes
    multiple_sep: ;
  - name: --outSAMheaderCommentFile
    type: string
    description: path to the file with @CO (comment) lines of the SAM header
  - name: --outSAMfilter
    type: string
    description: |-
      filter the output into main SAM/BAM files

      - KeepOnlyAddedReferences ... only keep the reads for which all alignments are to the extra reference sequences added with --genomeFastaFiles at the mapping stage.
      - KeepAllAddedReferences ...  keep all alignments to the extra reference sequences added with --genomeFastaFiles at the mapping stage.
    multiple: yes
    multiple_sep: ;
  - name: --outSAMmultNmax
    type: integer
    description: |-
      max number of multiple alignments for a read that will be output to the SAM/BAM files. Note that if this value is not equal to -1, the top scoring alignment will be output first

      - -1 ... all alignments (up to --outFilterMultimapNmax) will be output
    example: -1
  - name: --outSAMtlen
    type: integer
    description: |-
      calculation method for the TLEN field in the SAM/BAM files

      - 1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate
      - 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends
    example: 1
  - name: --outBAMcompression
    type: integer
    description: -1 to 10  BAM compression level, -1=default compression (6?), 0=no
      compression, 10=maximum compression
    example: 1
  - name: --outBAMsortingThreadN
    type: integer
    description: '>=0: number of threads for BAM sorting. 0 will default to min(6,--runThreadN).'
    example: 0
  - name: --outBAMsortingBinsN
    type: integer
    description: '>0:  number of genome bins for coordinate-sorting'
    example: 50
- name: BAM processing
  arguments:
  - name: --bamRemoveDuplicatesType
    type: string
    description: |-
      mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only

      - -                       ... no duplicate removal/marking
      - UniqueIdentical         ... mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical
      - UniqueIdenticalNotMulti  ... mark duplicate unique mappers but not multimappers.
  - name: --bamRemoveDuplicatesMate2basesN
    type: integer
    description: number of bases from the 5' of mate 2 to use in collapsing (e.g.
      for RAMPAGE)
    example: 0
- name: Output Wiggle
  arguments:
  - name: --outWigType
    type: string
    description: |-
      type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate .

      1st word:
      - None       ... no signal output
      - bedGraph   ... bedGraph format
      - wiggle     ... wiggle format
      2nd word:
      - read1_5p   ... signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc
      - read2      ... signal from only 2nd read
    multiple: yes
    multiple_sep: ;
  - name: --outWigStrand
    type: string
    description: |-
      strandedness of wiggle/bedGraph output

      - Stranded   ...  separate strands, str1 and str2
      - Unstranded ...  collapsed strands
    example: Stranded
  - name: --outWigReferencesPrefix
    type: string
    description: prefix matching reference names to include in the output wiggle file,
      e.g. "chr", default "-" - include all references
  - name: --outWigNorm
    type: string
    description: |-
      type of normalization for the signal

      - RPM    ... reads per million of mapped reads
      - None   ... no normalization, "raw" counts
    example: RPM
- name: Output Filtering
  arguments:
  - name: --outFilterType
    type: string
    description: |-
      type of filtering

      - Normal  ... standard filtering using only current alignment
      - BySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab
    example: Normal
  - name: --outFilterMultimapScoreRange
    type: integer
    description: the score range below the maximum score for multimapping alignments
    example: 1
  - name: --outFilterMultimapNmax
    type: integer
    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 .
    example: 10
  - name: --outFilterMismatchNmax
    type: integer
    description: alignment will be output only if it has no more mismatches than this
      value.
    example: 10
  - name: --outFilterMismatchNoverLmax
    type: double
    description: alignment will be output only if its ratio of mismatches to *mapped*
      length is less than or equal to this value.
    example: 0.3
  - name: --outFilterMismatchNoverReadLmax
    type: double
    description: alignment will be output only if its ratio of mismatches to *read*
      length is less than or equal to this value.
    example: 1.0
  - name: --outFilterScoreMin
    type: integer
    description: alignment will be output only if its score is higher than or equal
      to this value.
    example: 0
  - name: --outFilterScoreMinOverLread
    type: double
    description: same as outFilterScoreMin, but normalized to read length (sum of
      mates' lengths for paired-end reads)
    example: 0.66
  - name: --outFilterMatchNmin
    type: integer
    description: alignment will be output only if the number of matched bases is higher
      than or equal to this value.
    example: 0
  - name: --outFilterMatchNminOverLread
    type: double
    description: sam as outFilterMatchNmin, but normalized to the read length (sum
      of mates' lengths for paired-end reads).
    example: 0.66
  - name: --outFilterIntronMotifs
    type: string
    description: |-
      filter alignment using their motifs

      - 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.
  - name: --outFilterIntronStrands
    type: string
    description: |-
      filter alignments

      - RemoveInconsistentStrands      ... remove alignments that have junctions with inconsistent strands
      - None                           ... no filtering
    example: RemoveInconsistentStrands
- name: Output splice junctions (SJ.out.tab)
  arguments:
  - name: --outSJtype
    type: string
    description: |-
      type of splice junction output

      - Standard    ... standard SJ.out.tab output
      - None        ... no splice junction output
    example: Standard
- name: 'Output Filtering: Splice Junctions'
  arguments:
  - name: --outSJfilterReads
    type: string
    description: |-
      which reads to consider for collapsed splice junctions output

      - All     ... all reads, unique- and multi-mappers
      - Unique  ... uniquely mapping reads only
    example: All
  - name: --outSJfilterOverhangMin
    type: integer
    description: |-
      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
    example:
    - 30
    - 12
    - 12
    - 12
    multiple: yes
    multiple_sep: ;
  - name: --outSJfilterCountUniqueMin
    type: integer
    description: |-
      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
    example:
    - 3
    - 1
    - 1
    - 1
    multiple: yes
    multiple_sep: ;
  - name: --outSJfilterCountTotalMin
    type: integer
    description: |-
      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
    example:
    - 3
    - 1
    - 1
    - 1
    multiple: yes
    multiple_sep: ;
  - name: --outSJfilterDistToOtherSJmin
    type: integer
    description: |-
      minimum allowed distance to other junctions' donor/acceptor

      does not apply to annotated junctions
    example:
    - 10
    - 0
    - 5
    - 10
    multiple: yes
    multiple_sep: ;
  - name: --outSJfilterIntronMaxVsReadN
    type: integer
    description: |-
      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: <=200000. by >=4 reads any gap <=alignIntronMax
      does not apply to annotated junctions
    example:
    - 50000
    - 100000
    - 200000
    multiple: yes
    multiple_sep: ;
- name: Scoring
  arguments:
  - name: --scoreGap
    type: integer
    description: splice junction penalty (independent on intron motif)
    example: 0
  - name: --scoreGapNoncan
    type: integer
    description: non-canonical junction penalty (in addition to scoreGap)
    example: -8
  - name: --scoreGapGCAG
    type: integer
    description: GC/AG and CT/GC junction penalty (in addition to scoreGap)
    example: -4
  - name: --scoreGapATAC
    type: integer
    description: AT/AC  and GT/AT junction penalty  (in addition to scoreGap)
    example: -8
  - name: --scoreGenomicLengthLog2scale
    type: integer
    description: 'extra score logarithmically scaled with genomic length of the alignment:
      scoreGenomicLengthLog2scale*log2(genomicLength)'
    example: 0
  - name: --scoreDelOpen
    type: integer
    description: deletion open penalty
    example: -2
  - name: --scoreDelBase
    type: integer
    description: deletion extension penalty per base (in addition to scoreDelOpen)
    example: -2
  - name: --scoreInsOpen
    type: integer
    description: insertion open penalty
    example: -2
  - name: --scoreInsBase
    type: integer
    description: insertion extension penalty per base (in addition to scoreInsOpen)
    example: -2
  - name: --scoreStitchSJshift
    type: integer
    description: maximum score reduction while searching for SJ boundaries in the
      stitching step
    example: 1
- name: Alignments and Seeding
  arguments:
  - name: --seedSearchStartLmax
    type: integer
    description: defines the search start point through the read - the read is split
      into pieces no longer than this value
    example: 50
  - name: --seedSearchStartLmaxOverLread
    type: double
    description: seedSearchStartLmax normalized to read length (sum of mates' lengths
      for paired-end reads)
    example: 1.0
  - name: --seedSearchLmax
    type: integer
    description: defines the maximum length of the seeds, if =0 seed length is not
      limited
    example: 0
  - name: --seedMultimapNmax
    type: integer
    description: only pieces that map fewer than this value are utilized in the stitching
      procedure
    example: 10000
  - name: --seedPerReadNmax
    type: integer
    description: max number of seeds per read
    example: 1000
  - name: --seedPerWindowNmax
    type: integer
    description: max number of seeds per window
    example: 50
  - name: --seedNoneLociPerWindow
    type: integer
    description: max number of one seed loci per window
    example: 10
  - name: --seedSplitMin
    type: integer
    description: min length of the seed sequences split by Ns or mate gap
    example: 12
  - name: --seedMapMin
    type: integer
    description: min length of seeds to be mapped
    example: 5
  - name: --alignIntronMin
    type: integer
    description: minimum intron size, genomic gap is considered intron if its length>=alignIntronMin,
      otherwise it is considered Deletion
    example: 21
  - name: --alignIntronMax
    type: integer
    description: maximum intron size, if 0, max intron size will be determined by
      (2^winBinNbits)*winAnchorDistNbins
    example: 0
  - name: --alignMatesGapMax
    type: integer
    description: maximum gap between two mates, if 0, max intron gap will be determined
      by (2^winBinNbits)*winAnchorDistNbins
    example: 0
  - name: --alignSJoverhangMin
    type: integer
    description: minimum overhang (i.e. block size) for spliced alignments
    example: 5
  - name: --alignSJstitchMismatchNmax
    type: integer
    description: |-
      maximum number of mismatches for stitching of the splice junctions (-1: no limit).

      (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.
    example:
    - 0
    - -1
    - 0
    - 0
    multiple: yes
    multiple_sep: ;
  - name: --alignSJDBoverhangMin
    type: integer
    description: minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments
    example: 3
  - name: --alignSplicedMateMapLmin
    type: integer
    description: minimum mapped length for a read mate that is spliced
    example: 0
  - name: --alignSplicedMateMapLminOverLmate
    type: double
    description: alignSplicedMateMapLmin normalized to mate length
    example: 0.66
  - name: --alignWindowsPerReadNmax
    type: integer
    description: max number of windows per read
    example: 10000
  - name: --alignTranscriptsPerWindowNmax
    type: integer
    description: max number of transcripts per window
    example: 100
  - name: --alignTranscriptsPerReadNmax
    type: integer
    description: max number of different alignments per read to consider
    example: 10000
  - name: --alignEndsType
    type: string
    description: |-
      type of read ends alignment

      - 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
    example: Local
  - name: --alignEndsProtrude
    type: string
    description: |-
      allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate

      1st word: int: maximum number of protrusion bases allowed
      2nd word: string:
      -                     ConcordantPair ... report alignments with non-zero protrusion as concordant pairs
      -                     DiscordantPair ... report alignments with non-zero protrusion as discordant pairs
    example: 0    ConcordantPair
  - name: --alignSoftClipAtReferenceEnds
    type: string
    description: |-
      allow the soft-clipping of the alignments past the end of the chromosomes

      - Yes ... allow
      - No  ... prohibit, useful for compatibility with Cufflinks
    example: 'Yes'
  - name: --alignInsertionFlush
    type: string
    description: |-
      how to flush ambiguous insertion positions

      - None    ... insertions are not flushed
      - Right   ... insertions are flushed to the right
- name: Paired-End reads
  arguments:
  - name: --peOverlapNbasesMin
    type: integer
    description: minimum number of overlapping bases to trigger mates merging and
      realignment. Specify >0 value to switch on the "merginf of overlapping mates"
      algorithm.
    example: 0
  - name: --peOverlapMMp
    type: double
    description: maximum proportion of mismatched bases in the overlap area
    example: 0.01
- name: Windows, Anchors, Binning
  arguments:
  - name: --winAnchorMultimapNmax
    type: integer
    description: max number of loci anchors are allowed to map to
    example: 50
  - name: --winBinNbits
    type: integer
    description: =log2(winBin), where winBin is the size of the bin for the windows/clustering,
      each window will occupy an integer number of bins.
    example: 16
  - name: --winAnchorDistNbins
    type: integer
    description: max number of bins between two anchors that allows aggregation of
      anchors into one window
    example: 9
  - name: --winFlankNbins
    type: integer
    description: log2(winFlank), where win Flank is the size of the left and right
      flanking regions for each window
    example: 4
  - name: --winReadCoverageRelativeMin
    type: double
    description: minimum relative coverage of the read sequence by the seeds in a
      window, for STARlong algorithm only.
    example: 0.5
  - name: --winReadCoverageBasesMin
    type: integer
    description: minimum number of bases covered by the seeds in a window , for STARlong
      algorithm only.
    example: 0
- name: Chimeric Alignments
  arguments:
  - name: --chimOutType
    type: string
    description: |-
      type of chimeric output

      - Junctions       ... Chimeric.out.junction
      - SeparateSAMold  ... output old SAM into separate Chimeric.out.sam file
      - WithinBAM       ... output into main aligned BAM files (Aligned.*.bam)
      - WithinBAM HardClip  ... (default) hard-clipping in the CIGAR for supplemental chimeric alignments (default if no 2nd word is present)
      - WithinBAM SoftClip  ... soft-clipping in the CIGAR for supplemental chimeric alignments
    example: Junctions
    multiple: yes
    multiple_sep: ;
  - name: --chimSegmentMin
    type: integer
    description: minimum length of chimeric segment length, if ==0, no chimeric output
    example: 0
  - name: --chimScoreMin
    type: integer
    description: minimum total (summed) score of the chimeric segments
    example: 0
  - name: --chimScoreDropMax
    type: integer
    description: max drop (difference) of chimeric score (the sum of scores of all
      chimeric segments) from the read length
    example: 20
  - name: --chimScoreSeparation
    type: integer
    description: minimum difference (separation) between the best chimeric score and
      the next one
    example: 10
  - name: --chimScoreJunctionNonGTAG
    type: integer
    description: penalty for a non-GT/AG chimeric junction
    example: -1
  - name: --chimJunctionOverhangMin
    type: integer
    description: minimum overhang for a chimeric junction
    example: 20
  - name: --chimSegmentReadGapMax
    type: integer
    description: maximum gap in the read sequence between chimeric segments
    example: 0
  - name: --chimFilter
    type: string
    description: |-
      different filters for chimeric alignments

      - None ... no filtering
      - banGenomicN ... Ns are not allowed in the genome sequence around the chimeric junction
    example: banGenomicN
    multiple: yes
    multiple_sep: ;
  - name: --chimMainSegmentMultNmax
    type: integer
    description: maximum number of multi-alignments for the main chimeric segment.
      =1 will prohibit multimapping main segments.
    example: 10
  - name: --chimMultimapNmax
    type: integer
    description: |-
      maximum number of chimeric multi-alignments

      - 0 ... use the old scheme for chimeric detection which only considered unique alignments
    example: 0
  - name: --chimMultimapScoreRange
    type: integer
    description: the score range for multi-mapping chimeras below the best chimeric
      score. Only works with --chimMultimapNmax > 1
    example: 1
  - name: --chimNonchimScoreDropMin
    type: integer
    description: 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
    example: 20
  - name: --chimOutJunctionFormat
    type: integer
    description: |-
      formatting type for the Chimeric.out.junction file

      - 0 ... no comment lines/headers
      - 1 ... comment lines at the end of the file: command line and Nreads: total, unique/multi-mapping
    example: 0
- name: Quantification of Annotations
  arguments:
  - name: --quantMode
    type: string
    description: |-
      types of quantification requested

      - -                ... none
      - TranscriptomeSAM ... output SAM/BAM alignments to transcriptome into a separate file
      - GeneCounts       ... count reads per gene
    multiple: yes
    multiple_sep: ;
  - name: --quantTranscriptomeBAMcompression
    type: integer
    description: |-
      -2 to 10  transcriptome BAM compression level

      - -2  ... no BAM output
      - -1  ... default compression (6?)
      -  0  ... no compression
      -  10 ... maximum compression
    example: 1
  - name: --quantTranscriptomeSAMoutput
    type: string
    description: |-
      alignment filtering for TranscriptomeSAM output

      - BanSingleEnd_BanIndels_ExtendSoftclip ... prohibit indels and single-end alignments, extend softclips - compatible with RSEM
      - BanSingleEnd               ... prohibit single-end alignments, allow indels and softclips
      - BanSingleEnd_ExtendSoftclip ... prohibit single-end alignments, extend softclips, allow indels
    example: BanSingleEnd_BanIndels_ExtendSoftclip
- name: 2-pass Mapping
  arguments:
  - name: --twopassMode
    type: string
    description: |-
      2-pass mapping mode.

      - None        ... 1-pass mapping
      - Basic       ... basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly
  - name: --twopass1readsN
    type: integer
    description: number of reads to process for the 1st step. Use very large number
      (or default -1) to map all reads in the first step.
    example: -1
- name: WASP parameters
  arguments:
  - name: --waspOutputMode
    type: string
    description: |-
      WASP allele-specific output type. This is re-implementation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 1061-1063 (2015), https://www.nature.com/articles/nmeth.3582 .

      - SAMtag      ... add WASP tags to the alignments that pass WASP filtering
