Bwa mem + Samtools View

BwaMemSamtoolsView · 1 contributor · 1 version

No documentation was provided: contribute one

Quickstart

from janis_bioinformatics.tools.common.bwamem_samtoolsview import BwaMem_SamToolsView

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bwamemsamtoolsview_step",
    BwaMem_SamToolsView(
        reference=None,
        reads=None,
        sampleName=None,
    )
)
wf.output("out", source=bwamemsamtoolsview_step.out)

OR

  1. Install Janis
  2. Ensure Janis is configured to work with Docker or Singularity.
  3. Ensure all reference files are available:

Note

More information about these inputs are available below.

  1. Generate user input files for BwaMemSamtoolsView:
# user inputs
janis inputs BwaMemSamtoolsView > inputs.yaml

inputs.yaml

reads:
- reads_0.fastq.gz
- reads_1.fastq.gz
reference: reference.fasta
sampleName: <value>
  1. Run BwaMemSamtoolsView with:
janis run [...run options] \
    --inputs inputs.yaml \
    BwaMemSamtoolsView

Information

ID:BwaMemSamtoolsView
URL:No URL to the documentation was provided
Versions:0.7.17|1.9
Container:michaelfranklin/bwasamtools:0.7.17-1.9
Authors:Michael Franklin
Citations:None
Created:2019-05-10
Updated:2020-07-14

Outputs

name type documentation
out BAM  

Additional configuration (inputs)

name type prefix position documentation
reference FastaWithIndexes   2  
reads FastqGzPair   3  
sampleName String     Used to construct the readGroupHeaderLine with format: ‘@RGtID:{name}tSM:{name}tLB:{name}tPL:ILLUMINA’
mates Optional<FastqGzPair>   4  
outputFilename Optional<Filename> -o 8 output file name [stdout]
platformTechnology Optional<String>     (ReadGroup: PL) Used to construct the readGroupHeaderLine, defaults: ILLUMINA
minimumSeedLength Optional<Integer> -k 2 Matches shorter than INT will be missed. The alignment speed is usually insensitive to this value unless it significantly deviates 20. (Default: 19)
batchSize Optional<Integer> -K 2 Process INT input bases in each batch regardless of the number of threads in use [10000000*nThreads]. By default, the batch size is proportional to the number of threads in use. Because the inferred insert size distribution slightly depends on the batch size, using different number of threads may produce different output. Specifying this option helps reproducibility.
useSoftClippingForSupplementaryAlignments Optional<Boolean> -Y 2 Use soft clipping CIGAR operation for supplementary alignments. By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments.
bandwidth Optional<Integer> -w 2 Essentially, gaps longer than ${bandWidth} will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. (Default: 100)
offDiagonalXDropoff Optional<Integer> -d 2 (Z-dropoff): Stop extension when the difference between the best and the current extension score is above |i-j|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST’s X-dropoff except that it doesn’t penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. (Default: 100)
reseedTrigger Optional<Float> -r 2 Trigger re-seeding for a MEM longer than minSeedLen*FLOAT. This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy. (Default: 1.5)
occurenceDiscard Optional<Integer> -c 2 Discard a MEM if it has more than INT occurence in the genome. This is an insensitive parameter. (Default: 10000)
performSW Optional<Boolean> -P 2 In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.
matchingScore Optional<Integer> -A 2 Matching score. (Default: 1)
mismatchPenalty Optional<Integer> -B 2 Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. (Default: 4)
openGapPenalty Optional<Integer> -O 2 Gap open penalty. (Default: 6)
gapExtensionPenalty Optional<Integer> -E 2 Gap extension penalty. A gap of length k costs O + k*E (i.e. -O is for opening a zero-length gap). (Default: 1)
clippingPenalty Optional<Integer> -L 2 Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best SW score; clipping penalty is not deducted. (Default: 5)
unpairedReadPenalty Optional<Integer> -U 2 Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. (Default: 9)
assumeInterleavedFirstInput Optional<Boolean> -p 2 Assume the first input query file is interleaved paired-end FASTA/Q.
outputAlignmentThreshold Optional<Integer> -T 2 Don’t output alignment with score lower than INT. Only affects output. (Default: 30)
outputAllElements Optional<Boolean> -a 2 Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments.
appendComments Optional<Boolean> -C 2 Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
hardClipping Optional<Boolean> -H 2 Use hard clipping ’H’ in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.
markShorterSplits Optional<Boolean> -M 2 Mark shorter split hits as secondary (for Picard compatibility).
verboseLevel Optional<Integer> -v 2 Control the verbose level of the output. This option has not been fully supported throughout BWA. Ideally, a value: 0 for disabling all the output to stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for all normal messages; 4 or higher for debugging. When this option takes value 4, the output is not SAM. (Default: 3)
skippedReadsOutputFilename Optional<String> -U 8 output reads not selected by filters to FILE [null]
referenceIndex Optional<File> -t 8 FILE listing reference names and lengths (see long help) [null]
intervals Optional<bed> -L 8 only include reads overlapping this BED FILE [null]
includeReadsInReadGroup Optional<String> -r 8 only include reads in read group STR [null]
includeReadsInFile Optional<File> -R 8 only include reads with read group listed in FILE [null]
includeReadsWithQuality Optional<Integer> -q 8 only include reads with mapping quality >= INT [0]
includeReadsInLibrary Optional<String> -l 8 only include reads in library STR [null]
includeReadsWithCIGAROps Optional<Integer> -m 8 only include reads with number of CIGAR operations consuming query sequence >= INT [0]
includeReadsWithAllFLAGs Optional<Array<Integer>> -f 8 only include reads with all of the FLAGs in INT present [0]
includeReadsWithoutFLAGs Optional<Array<Integer>> -F 8 only include reads with none of the FLAGS in INT present [0]
excludeReadsWithAllFLAGs Optional<Array<Integer>> -G 8 only EXCLUDE reads with all of the FLAGs in INT present [0] fraction of templates/read pairs to keep; INT part sets seed)
useMultiRegionIterator Optional<Boolean> -M 8 use the multi-region iterator (increases the speed, removes duplicates and outputs the reads as they are ordered in the file)
readTagToStrip Optional<String> -x 8 read tag to strip (repeatable) [null]
collapseBackwardCIGAROps Optional<Boolean> -B 8 collapse the backward CIGAR operation Specify a single input file format option in the form of OPTION or OPTION=VALUE
outputFmt Optional<String> –output-fmt 8 (OPT[, -O) Specify output format (SAM, BAM, CRAM) Specify a single output file format option in the form of OPTION or OPTION=VALUE

Workflow Description Language

version development

task BwaMemSamtoolsView {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    File reference
    File reference_fai
    File reference_amb
    File reference_ann
    File reference_bwt
    File reference_pac
    File reference_sa
    File reference_dict
    Array[File] reads
    Array[File]? mates
    String? outputFilename
    String sampleName
    String? platformTechnology
    Int? minimumSeedLength
    Int? batchSize
    Boolean? useSoftClippingForSupplementaryAlignments
    Int? bandwidth
    Int? offDiagonalXDropoff
    Float? reseedTrigger
    Int? occurenceDiscard
    Boolean? performSW
    Int? matchingScore
    Int? mismatchPenalty
    Int? openGapPenalty
    Int? gapExtensionPenalty
    Int? clippingPenalty
    Int? unpairedReadPenalty
    Boolean? assumeInterleavedFirstInput
    Int? outputAlignmentThreshold
    Boolean? outputAllElements
    Boolean? appendComments
    Boolean? hardClipping
    Boolean? markShorterSplits
    Int? verboseLevel
    String? skippedReadsOutputFilename
    File? referenceIndex
    File? intervals
    String? includeReadsInReadGroup
    File? includeReadsInFile
    Int? includeReadsWithQuality
    String? includeReadsInLibrary
    Int? includeReadsWithCIGAROps
    Array[Int]? includeReadsWithAllFLAGs
    Array[Int]? includeReadsWithoutFLAGs
    Array[Int]? excludeReadsWithAllFLAGs
    Boolean? useMultiRegionIterator
    String? readTagToStrip
    Boolean? collapseBackwardCIGAROps
    String? outputFmt
  }
  command <<<
    set -e
     \
      bwa \
      mem \
      ~{reference} \
      ~{if defined(minimumSeedLength) then ("-k " + minimumSeedLength) else ''} \
      ~{if defined(batchSize) then ("-K " + batchSize) else ''} \
      ~{if (defined(useSoftClippingForSupplementaryAlignments) && select_first([useSoftClippingForSupplementaryAlignments])) then "-Y" else ""} \
      ~{if defined(bandwidth) then ("-w " + bandwidth) else ''} \
      ~{if defined(offDiagonalXDropoff) then ("-d " + offDiagonalXDropoff) else ''} \
      ~{if defined(reseedTrigger) then ("-r " + reseedTrigger) else ''} \
      ~{if defined(occurenceDiscard) then ("-c " + occurenceDiscard) else ''} \
      ~{if (defined(performSW) && select_first([performSW])) then "-P" else ""} \
      ~{if defined(matchingScore) then ("-A " + matchingScore) else ''} \
      ~{if defined(mismatchPenalty) then ("-B " + mismatchPenalty) else ''} \
      ~{if defined(openGapPenalty) then ("-O " + openGapPenalty) else ''} \
      ~{if defined(gapExtensionPenalty) then ("-E " + gapExtensionPenalty) else ''} \
      ~{if defined(clippingPenalty) then ("-L " + clippingPenalty) else ''} \
      ~{if defined(unpairedReadPenalty) then ("-U " + unpairedReadPenalty) else ''} \
      ~{if (defined(assumeInterleavedFirstInput) && select_first([assumeInterleavedFirstInput])) then "-p" else ""} \
      ~{if defined(outputAlignmentThreshold) then ("-T " + outputAlignmentThreshold) else ''} \
      ~{if (defined(outputAllElements) && select_first([outputAllElements])) then "-a" else ""} \
      ~{if (defined(appendComments) && select_first([appendComments])) then "-C" else ""} \
      ~{if (defined(hardClipping) && select_first([hardClipping])) then "-H" else ""} \
      ~{if (defined(markShorterSplits) && select_first([markShorterSplits])) then "-M" else ""} \
      ~{if defined(verboseLevel) then ("-v " + verboseLevel) else ''} \
      -R '@RG\tID:~{sampleName}\tSM:~{sampleName}\tLB:~{sampleName}\tPL:~{select_first([platformTechnology, "ILLUMINA"])}' \
      -t ~{select_first([runtime_cpu, 16, 1])} \
      ~{if length(reads) > 0 then sep(" ", reads) else ""} \
      ~{if (defined(mates) && length(select_first([mates])) > 0) then sep(" ", select_first([mates])) else ""} \
      | \
      samtools \
      view \
      -o ~{select_first([outputFilename, "~{sampleName}.bam"])} \
      ~{if defined(skippedReadsOutputFilename) then ("-U " + skippedReadsOutputFilename) else ''} \
      ~{if defined(referenceIndex) then ("-t " + referenceIndex) else ''} \
      ~{if defined(intervals) then ("-L " + intervals) else ''} \
      ~{if defined(includeReadsInReadGroup) then ("-r " + includeReadsInReadGroup) else ''} \
      ~{if defined(includeReadsInFile) then ("-R " + includeReadsInFile) else ''} \
      ~{if defined(includeReadsWithQuality) then ("-q " + includeReadsWithQuality) else ''} \
      ~{if defined(includeReadsInLibrary) then ("-l " + includeReadsInLibrary) else ''} \
      ~{if defined(includeReadsWithCIGAROps) then ("-m " + includeReadsWithCIGAROps) else ''} \
      ~{if (defined(includeReadsWithAllFLAGs) && length(select_first([includeReadsWithAllFLAGs])) > 0) then "-f " + sep(" ", select_first([includeReadsWithAllFLAGs])) else ""} \
      ~{if (defined(includeReadsWithoutFLAGs) && length(select_first([includeReadsWithoutFLAGs])) > 0) then "-F " + sep(" ", select_first([includeReadsWithoutFLAGs])) else ""} \
      ~{if (defined(excludeReadsWithAllFLAGs) && length(select_first([excludeReadsWithAllFLAGs])) > 0) then "-G " + sep(" ", select_first([excludeReadsWithAllFLAGs])) else ""} \
      ~{if (defined(useMultiRegionIterator) && select_first([useMultiRegionIterator])) then "-M" else ""} \
      ~{if defined(readTagToStrip) then ("-x " + readTagToStrip) else ''} \
      ~{if (defined(collapseBackwardCIGAROps) && select_first([collapseBackwardCIGAROps])) then "-B" else ""} \
      ~{if defined(outputFmt) then ("--output-fmt " + outputFmt) else ''} \
      -T ~{reference} \
      --threads ~{select_first([runtime_cpu, 16, 1])} \
      -h \
      -b
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 16, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "michaelfranklin/bwasamtools:0.7.17-1.9"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 16, 4])}G"
    preemptible: 2
  }
  output {
    File out = select_first([outputFilename, "~{sampleName}.bam"])
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Bwa mem + Samtools View

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: michaelfranklin/bwasamtools:0.7.17-1.9

inputs:
- id: reference
  label: reference
  type: File
  secondaryFiles:
  - pattern: .fai
  - pattern: .amb
  - pattern: .ann
  - pattern: .bwt
  - pattern: .pac
  - pattern: .sa
  - pattern: ^.dict
  inputBinding:
    position: 2
    shellQuote: false
- id: reads
  label: reads
  type:
    type: array
    items: File
  inputBinding:
    position: 3
    shellQuote: false
- id: mates
  label: mates
  type:
  - type: array
    items: File
  - 'null'
  inputBinding:
    position: 4
    itemSeparator: ' '
    shellQuote: false
- id: outputFilename
  label: outputFilename
  doc: output file name [stdout]
  type:
  - string
  - 'null'
  default: generated.bam
  inputBinding:
    prefix: -o
    position: 8
    valueFrom: $(inputs.sampleName).bam
    shellQuote: false
- id: sampleName
  label: sampleName
  doc: |-
    Used to construct the readGroupHeaderLine with format: '@RG\tID:{name}\tSM:{name}\tLB:{name}\tPL:ILLUMINA'
  type: string
- id: platformTechnology
  label: platformTechnology
  doc: '(ReadGroup: PL) Used to construct the readGroupHeaderLine, defaults: ILLUMINA'
  type: string
  default: ILLUMINA
- id: minimumSeedLength
  label: minimumSeedLength
  doc: |-
    Matches shorter than INT will be missed. The alignment speed is usually insensitive to this value unless it significantly deviates 20. (Default: 19)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -k
    position: 2
    shellQuote: false
- id: batchSize
  label: batchSize
  doc: |-
    Process INT input bases in each batch regardless of the number of threads in use [10000000*nThreads]. By default, the batch size is proportional to the number of threads in use. Because the inferred insert size distribution slightly depends on the batch size, using different number of threads may produce different output. Specifying this option helps reproducibility.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -K
    position: 2
    shellQuote: false
- id: useSoftClippingForSupplementaryAlignments
  label: useSoftClippingForSupplementaryAlignments
  doc: |-
    Use soft clipping CIGAR operation for supplementary alignments. By default, BWA-MEM uses soft clipping for the primary alignment and hard clipping for supplementary alignments.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -Y
    position: 2
    shellQuote: false
- id: bandwidth
  label: bandwidth
  doc: |-
    Essentially, gaps longer than ${bandWidth} will not be found. Note that the maximum gap length is also affected by the scoring matrix and the hit length, not solely determined by this option. (Default: 100)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -w
    position: 2
    shellQuote: false
- id: offDiagonalXDropoff
  label: offDiagonalXDropoff
  doc: |-
    (Z-dropoff): Stop extension when the difference between the best and the current extension score is above |i-j|*A+INT, where i and j are the current positions of the query and reference, respectively, and A is the matching score. Z-dropoff is similar to BLAST’s X-dropoff except that it doesn’t penalize gaps in one of the sequences in the alignment. Z-dropoff not only avoids unnecessary extension, but also reduces poor alignments inside a long good alignment. (Default: 100)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -d
    position: 2
    shellQuote: false
- id: reseedTrigger
  label: reseedTrigger
  doc: |-
    Trigger re-seeding for a MEM longer than minSeedLen*FLOAT. This is a key heuristic parameter for tuning the performance. Larger value yields fewer seeds, which leads to faster alignment speed but lower accuracy. (Default: 1.5)
  type:
  - float
  - 'null'
  inputBinding:
    prefix: -r
    position: 2
    shellQuote: false
- id: occurenceDiscard
  label: occurenceDiscard
  doc: |-
    Discard a MEM if it has more than INT occurence in the genome. This is an insensitive parameter. (Default: 10000)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -c
    position: 2
    shellQuote: false
- id: performSW
  label: performSW
  doc: |-
    In the paired-end mode, perform SW to rescue missing hits only but do not try to find hits that fit a proper pair.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -P
    position: 2
    shellQuote: false
- id: matchingScore
  label: matchingScore
  doc: 'Matching score. (Default: 1)'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -A
    position: 2
    shellQuote: false
- id: mismatchPenalty
  label: mismatchPenalty
  doc: |-
    Mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. (Default: 4)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -B
    position: 2
    shellQuote: false
- id: openGapPenalty
  label: openGapPenalty
  doc: 'Gap open penalty. (Default: 6)'
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -O
    position: 2
    shellQuote: false
- id: gapExtensionPenalty
  label: gapExtensionPenalty
  doc: |-
    Gap extension penalty. A gap of length k costs O + k*E (i.e. -O is for opening a zero-length gap). (Default: 1)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -E
    position: 2
    shellQuote: false
- id: clippingPenalty
  label: clippingPenalty
  doc: |-
    Clipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best SW score; clipping penalty is not deducted. (Default: 5)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -L
    position: 2
    shellQuote: false
- id: unpairedReadPenalty
  label: unpairedReadPenalty
  doc: |-
    Penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. (Default: 9)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -U
    position: 2
    shellQuote: false
- id: assumeInterleavedFirstInput
  label: assumeInterleavedFirstInput
  doc: 'Assume the first input query file is interleaved paired-end FASTA/Q. '
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -p
    position: 2
    shellQuote: false
- id: outputAlignmentThreshold
  label: outputAlignmentThreshold
  doc: |-
    Don’t output alignment with score lower than INT. Only affects output. (Default: 30)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -T
    position: 2
    shellQuote: false
- id: outputAllElements
  label: outputAllElements
  doc: |-
    Output all found alignments for single-end or unpaired paired-end reads. These alignments will be flagged as secondary alignments.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -a
    position: 2
    shellQuote: false
- id: appendComments
  label: appendComments
  doc: |-
    Append append FASTA/Q comment to SAM output. This option can be used to transfer read meta information (e.g. barcode) to the SAM output. Note that the FASTA/Q comment (the string after a space in the header line) must conform the SAM spec (e.g. BC:Z:CGTAC). Malformated comments lead to incorrect SAM output.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -C
    position: 2
    shellQuote: false
- id: hardClipping
  label: hardClipping
  doc: |-
    Use hard clipping ’H’ in the SAM output. This option may dramatically reduce the redundancy of output when mapping long contig or BAC sequences.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -H
    position: 2
    shellQuote: false
- id: markShorterSplits
  label: markShorterSplits
  doc: Mark shorter split hits as secondary (for Picard compatibility).
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -M
    position: 2
    shellQuote: false
- id: verboseLevel
  label: verboseLevel
  doc: |-
    Control the verbose level of the output. This option has not been fully supported throughout BWA. Ideally, a value: 0 for disabling all the output to stderr; 1 for outputting errors only; 2 for warnings and errors; 3 for all normal messages; 4 or higher for debugging. When this option takes value 4, the output is not SAM. (Default: 3)
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -v
    position: 2
    shellQuote: false
- id: skippedReadsOutputFilename
  label: skippedReadsOutputFilename
  doc: output reads not selected by filters to FILE [null]
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -U
    position: 8
    shellQuote: false
- id: referenceIndex
  label: referenceIndex
  doc: FILE listing reference names and lengths (see long help) [null]
  type:
  - File
  - 'null'
  inputBinding:
    prefix: -t
    position: 8
    shellQuote: false
- id: intervals
  label: intervals
  doc: only include reads overlapping this BED FILE [null]
  type:
  - File
  - 'null'
  inputBinding:
    prefix: -L
    position: 8
    shellQuote: false
- id: includeReadsInReadGroup
  label: includeReadsInReadGroup
  doc: only include reads in read group STR [null]
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -r
    position: 8
    shellQuote: false
- id: includeReadsInFile
  label: includeReadsInFile
  doc: only include reads with read group listed in FILE [null]
  type:
  - File
  - 'null'
  inputBinding:
    prefix: -R
    position: 8
    shellQuote: false
- id: includeReadsWithQuality
  label: includeReadsWithQuality
  doc: only include reads with mapping quality >= INT [0]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -q
    position: 8
    shellQuote: false
- id: includeReadsInLibrary
  label: includeReadsInLibrary
  doc: only include reads in library STR [null]
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -l
    position: 8
    shellQuote: false
- id: includeReadsWithCIGAROps
  label: includeReadsWithCIGAROps
  doc: |-
    only include reads with number of CIGAR operations consuming query sequence >= INT [0]
  type:
  - int
  - 'null'
  inputBinding:
    prefix: -m
    position: 8
    shellQuote: false
- id: includeReadsWithAllFLAGs
  label: includeReadsWithAllFLAGs
  doc: only include reads with all of the FLAGs in INT present [0]
  type:
  - type: array
    items: int
  - 'null'
  inputBinding:
    prefix: -f
    position: 8
    itemSeparator: ' '
    shellQuote: false
- id: includeReadsWithoutFLAGs
  label: includeReadsWithoutFLAGs
  doc: only include reads with none of the FLAGS in INT present [0]
  type:
  - type: array
    items: int
  - 'null'
  inputBinding:
    prefix: -F
    position: 8
    itemSeparator: ' '
    shellQuote: false
- id: excludeReadsWithAllFLAGs
  label: excludeReadsWithAllFLAGs
  doc: |-
    only EXCLUDE reads with all of the FLAGs in INT present [0] fraction of templates/read pairs to keep; INT part sets seed)
  type:
  - type: array
    items: int
  - 'null'
  inputBinding:
    prefix: -G
    position: 8
    itemSeparator: ' '
    shellQuote: false
- id: useMultiRegionIterator
  label: useMultiRegionIterator
  doc: |-
    use the multi-region iterator (increases the speed, removes duplicates and outputs the reads as they are ordered in the file)
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -M
    position: 8
    shellQuote: false
- id: readTagToStrip
  label: readTagToStrip
  doc: read tag to strip (repeatable) [null]
  type:
  - string
  - 'null'
  inputBinding:
    prefix: -x
    position: 8
    shellQuote: false
- id: collapseBackwardCIGAROps
  label: collapseBackwardCIGAROps
  doc: |-
    collapse the backward CIGAR operation Specify a single input file format option in the form of OPTION or OPTION=VALUE
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: -B
    position: 8
    shellQuote: false
- id: outputFmt
  label: outputFmt
  doc: |-
    (OPT[, -O)  Specify output format (SAM, BAM, CRAM) Specify a single output file format option in the form of OPTION or OPTION=VALUE
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --output-fmt
    position: 8
    shellQuote: false

outputs:
- id: out
  label: out
  type: File
  outputBinding:
    glob: $(inputs.sampleName).bam
    loadContents: false
stdout: _stdout
stderr: _stderr
arguments:
- position: 0
  valueFrom: bwa
  shellQuote: false
- position: 1
  valueFrom: mem
  shellQuote: false
- position: 5
  valueFrom: '|'
  shellQuote: false
- position: 6
  valueFrom: samtools
  shellQuote: false
- position: 7
  valueFrom: view
  shellQuote: false
- prefix: -T
  position: 8
  valueFrom: $(inputs.reference)
  shellQuote: false
- prefix: --threads
  position: 8
  valueFrom: |-
    $([inputs.runtime_cpu, 16, 1].filter(function (inner) { return inner != null })[0])
  shellQuote: false
- position: 8
  valueFrom: -h
  shellQuote: false
- position: 8
  valueFrom: -b
  shellQuote: false
- prefix: -R
  position: 2
  valueFrom: |-
    $("@RG\\tID:{name}\\tSM:{name}\\tLB:{name}\\tPL:{pl}".replace(/\{name\}/g, inputs.sampleName).replace(/\{pl\}/g, inputs.platformTechnology))
- prefix: -t
  position: 2
  valueFrom: |-
    $([inputs.runtime_cpu, 16, 1].filter(function (inner) { return inner != null })[0])
  shellQuote: false

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: BwaMemSamtoolsView