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Bcl2Fastq

bcl2fastq · 1 contributor · 1 version

BCL to FASTQ file converter

Warning

Bcl2Fastq did not include a container. You can provide one through the command line by including the following instruction:

janis run --container-override 'bcl2fastq=<organisation/container:version>' bcl2fastq

Quickstart

from janis_bioinformatics.tools.illumina.bcl2fastq.versions import Bcl2Fastq_2_20_0

wf = WorkflowBuilder("myworkflow")

wf.step(
    "bcl2fastq_step",
    Bcl2Fastq_2_20_0(
        runFolderDir=None,
        sampleSheet=None,
        loadingThreads=None,
        processingThreads=None,
        writingThreads=None,
    )
)
wf.output("unalignedReads", source=bcl2fastq_step.unalignedReads)
wf.output("stats", source=bcl2fastq_step.stats)
wf.output("interop", source=bcl2fastq_step.interop)

OR

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

Note

More information about these inputs are available below.

Generate user input files for bcl2fastq:

# user inputs
janis inputs bcl2fastq > inputs.yaml

inputs.yaml

runFolderDir: null
sampleSheet: sampleSheet.csv

Run bcl2fastq with:

janis run [...run options] \
    --inputs inputs.yaml \
    --container-override 'bcl2fastq=<organisation/container:version>' \
    bcl2fastq

Information

ID: bcl2fastq
URL: https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
Versions: 2.20.0
Container: None
Authors: Matthias De Smet (@mattdsm)
Citations: None
Created: 2020-03-05
Updated: 2020-03-05

Outputs

name	type	documentation
unalignedReads stats interop	Array<FastqGz> Array<File> Array<File>

Additional configuration (inputs)

name	type	prefix	position	documentation
runFolderDir sampleSheet loadingThreads processingThreads writingThreads minimumTrimmedReadLength useBasesMask maskShortAdapterReads adapterStringency ignoreMissingBcls ignoreMissingFilter ignoreMissingPositions writeFastqReverseComplement withFailedReads createFastqForIndexReads findAdaptersWithSlidingWindow noBgzfCompression barcodeMismatches noLaneSplitting	Directory csv Integer Integer Integer Optional<Integer> Optional<String> Optional<Integer> Optional<Float> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Boolean> Optional<Integer> Optional<Boolean>	-R --sample-sheet -r -p -w --minimum-trimmed-read-length --use-bases-mask --mask-short-adapter-reads --adapter-stringency --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --write-fastq-reverse-complement --with-failed-reads --create-fastq-for-index-reads --find-adapters-with-sliding-window --no-bgzf-compression --barcode-mismatches --no-lane-splitting		path to runfolder directory path to the sample sheet number of threads used for loading BCL data number of threads used for processing demultiplexed data number of threads used for writing FASTQ data minimum read length after adapter trimming specifies how to use each cycle smallest number of remaining bases (after masking bases below the minimum trimmed read length) below which whole read is masked adapter stringency assume 'N'/'#' for missing calls assume 'true' for missing filters assume [0,i] for missing positions, where i is incremented starting from 0 generate FASTQs containing reverse complements of actual data include non-PF clusters create FASTQ files also for index reads find adapters with simple sliding window algorithm turn off BGZF compression for FASTQ files number of allowed mismatches per index do not split fastq files by lane

Workflow Description Language

version development

task bcl2fastq {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Directory runFolderDir
    File sampleSheet
    Int? loadingThreads
    Int? processingThreads
    Int? writingThreads
    Int? minimumTrimmedReadLength
    String? useBasesMask
    Int? maskShortAdapterReads
    Float? adapterStringency
    Boolean? ignoreMissingBcls
    Boolean? ignoreMissingFilter
    Boolean? ignoreMissingPositions
    Boolean? writeFastqReverseComplement
    Boolean? withFailedReads
    Boolean? createFastqForIndexReads
    Boolean? findAdaptersWithSlidingWindow
    Boolean? noBgzfCompression
    Int? barcodeMismatches
    Boolean? noLaneSplitting
  }
  command <<<
    set -e
    bcl2fastq \
      -R '~{runFolderDir}' \
      --sample-sheet '~{sampleSheet}' \
      -r ~{select_first([loadingThreads, 4])} \
      -p ~{select_first([processingThreads, 4])} \
      -w ~{select_first([writingThreads, 4])} \
      ~{if defined(minimumTrimmedReadLength) then ("--minimum-trimmed-read-length " + minimumTrimmedReadLength) else ''} \
      ~{if defined(useBasesMask) then ("--use-bases-mask '" + useBasesMask + "'") else ""} \
      ~{if defined(maskShortAdapterReads) then ("--mask-short-adapter-reads " + maskShortAdapterReads) else ''} \
      ~{if defined(adapterStringency) then ("--adapter-stringency " + adapterStringency) else ''} \
      ~{if (defined(ignoreMissingBcls) && select_first([ignoreMissingBcls])) then "--ignore-missing-bcls" else ""} \
      ~{if (defined(ignoreMissingFilter) && select_first([ignoreMissingFilter])) then "--ignore-missing-filter" else ""} \
      ~{if (defined(ignoreMissingPositions) && select_first([ignoreMissingPositions])) then "--ignore-missing-positions" else ""} \
      ~{if (defined(writeFastqReverseComplement) && select_first([writeFastqReverseComplement])) then "--write-fastq-reverse-complement" else ""} \
      ~{if (defined(withFailedReads) && select_first([withFailedReads])) then "--with-failed-reads" else ""} \
      ~{if (defined(createFastqForIndexReads) && select_first([createFastqForIndexReads])) then "--create-fastq-for-index-reads" else ""} \
      ~{if (defined(findAdaptersWithSlidingWindow) && select_first([findAdaptersWithSlidingWindow])) then "--find-adapters-with-sliding-window" else ""} \
      ~{if (defined(noBgzfCompression) && select_first([noBgzfCompression])) then "--no-bgzf-compression" else ""} \
      ~{if defined(barcodeMismatches) then ("--barcode-mismatches " + barcodeMismatches) else ''} \
      ~{if (defined(noLaneSplitting) && select_first([noLaneSplitting])) then " --no-lane-splitting" else ""} \
      --output-dir '.'
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 4, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4, 4])}G"
    preemptible: 2
  }
  output {
    Array[File] unalignedReads = glob("*/*.fastq.gz")
    Array[File] stats = glob("Stats/*")
    Array[File] interop = glob("InterOp/*")
  }
}

Common Workflow Language

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Bcl2Fastq
doc: BCL to FASTQ file converter

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement

inputs:
- id: runFolderDir
  label: runFolderDir
  doc: path to runfolder directory
  type: Directory
  inputBinding:
    prefix: -R
- id: sampleSheet
  label: sampleSheet
  doc: path to the sample sheet
  type: File
  inputBinding:
    prefix: --sample-sheet
- id: loadingThreads
  label: loadingThreads
  doc: number of threads used for loading BCL data
  type: int
  default: 4
  inputBinding:
    prefix: -r
- id: processingThreads
  label: processingThreads
  doc: number of threads used for processing demultiplexed data
  type: int
  default: 4
  inputBinding:
    prefix: -p
- id: writingThreads
  label: writingThreads
  doc: number of threads used for writing FASTQ data
  type: int
  default: 4
  inputBinding:
    prefix: -w
- id: minimumTrimmedReadLength
  label: minimumTrimmedReadLength
  doc: minimum read length after adapter trimming
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --minimum-trimmed-read-length
- id: useBasesMask
  label: useBasesMask
  doc: specifies how to use each cycle
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --use-bases-mask
- id: maskShortAdapterReads
  label: maskShortAdapterReads
  doc: |-
    smallest number of remaining bases (after masking bases below the minimum trimmed read length) below which whole read is masked
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --mask-short-adapter-reads
- id: adapterStringency
  label: adapterStringency
  doc: adapter stringency
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --adapter-stringency
- id: ignoreMissingBcls
  label: ignoreMissingBcls
  doc: assume 'N'/'#' for missing calls
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --ignore-missing-bcls
- id: ignoreMissingFilter
  label: ignoreMissingFilter
  doc: assume 'true' for missing filters
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --ignore-missing-filter
- id: ignoreMissingPositions
  label: ignoreMissingPositions
  doc: assume [0,i] for missing positions, where i is incremented starting from 0
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --ignore-missing-positions
- id: writeFastqReverseComplement
  label: writeFastqReverseComplement
  doc: generate FASTQs containing reverse complements of actual data
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --write-fastq-reverse-complement
- id: withFailedReads
  label: withFailedReads
  doc: include non-PF clusters
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --with-failed-reads
- id: createFastqForIndexReads
  label: createFastqForIndexReads
  doc: create FASTQ files also for index reads
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --create-fastq-for-index-reads
- id: findAdaptersWithSlidingWindow
  label: findAdaptersWithSlidingWindow
  doc: find adapters with simple sliding window algorithm
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --find-adapters-with-sliding-window
- id: noBgzfCompression
  label: noBgzfCompression
  doc: turn off BGZF compression for FASTQ files
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --no-bgzf-compression
- id: barcodeMismatches
  label: barcodeMismatches
  doc: number of allowed mismatches per index
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --barcode-mismatches
- id: noLaneSplitting
  label: noLaneSplitting
  doc: do not split fastq files by lane
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: ' --no-lane-splitting'

outputs:
- id: unalignedReads
  label: unalignedReads
  type:
    type: array
    items: File
  outputBinding:
    glob: '*/*.fastq.gz'
    loadContents: false
- id: stats
  label: stats
  type:
    type: array
    items: File
  outputBinding:
    glob: Stats/*
    loadContents: false
- id: interop
  label: interop
  type:
    type: array
    items: File
  outputBinding:
    glob: InterOp/*
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand: bcl2fastq
arguments:
- prefix: --output-dir
  position: 0
  valueFrom: .

hints:
- class: ToolTimeLimit
  timelimit: |-
    $([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: bcl2fastq

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Bcl2Fastq

Quickstart

Information

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Additional configuration (inputs)

Workflow Description Language

Common Workflow Language

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Bcl2Fastq

Quickstart

Information

Outputs

Additional configuration (inputs)

Workflow Description Language

Common Workflow Language