CellRanger mkfastq¶

CellRangerMkfastq · 1 contributor · 1 version

/opt/cellranger-3.0.2/cellranger-cs/3.0.2/bin cellranger mkfastq (3.0.2) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ——————————————————————————- Run Illumina demultiplexer on sample sheets that contain 10x-specific sample index sets, and generate 10x-specific quality metrics after the demultiplex. Any bcl2fastq argument will work (except a few that are set by the pipeline to ensure proper trimming and sample indexing). The FASTQ output generated will be the same as when running bcl2fastq directly. These bcl2fastq arguments are overridden by this pipeline:

–fastq-cluster-count –minimum-trimmed-read-length –mask-short-adapter-reads

Usage:: cellranger mkfastq –run=PATH [options] cellranger mkfastq -h | –help | –version

Quickstart¶

from janis_bioinformatics.tools.cellranger.mkfastq.versions import CellRangerMkfastq_3_0_2

wf = WorkflowBuilder("myworkflow")

wf.step(
    "cellrangermkfastq_step",
    CellRangerMkfastq_3_0_2(
        run=None,
    )
)
wf.output("out", source=cellrangermkfastq_step.out)

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 CellRangerMkfastq:

# user inputs
janis inputs CellRangerMkfastq > inputs.yaml

inputs.yaml

run: null

Run CellRangerMkfastq with:

janis run [...run options] \
    --inputs inputs.yaml \
    CellRangerMkfastq

Information¶

ID:	`CellRangerMkfastq`
URL:	No URL to the documentation was provided
Versions:	v3.0.2
Container:	fbrundu/cellranger:v3.0.2
Authors:	Michael Franklin
Citations:	None
Created:	2019-10-24
Updated:	2019-10-24

Outputs¶

name	type	documentation
out	Directory

Additional configuration (inputs)¶

name	type	prefix	documentation
run	Directory	–run=	Path of Illumina BCL run folder.
id	Optional<String>	–id=	Name of the folder created by mkfastq. If not supplied, will default to the name of the flowcell referred to by the –run argument.
outputFoldername	Optional<Filename>	–output-dir=	Same as in bcl2fastq. Folder where FASTQs, reports and stats will be generated.
csv	Optional<csv>	–csv=	Apparently the same as sampleSheet. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet. Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).
sampleSheet	Optional<File>	–sample-sheet=	(–samplesheet= \| –csv=) Path to the sample sheet. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet. Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).
ignoreDualIndex	Optional<Boolean>	–ignore-dual-index	On a dual-indexed flowcell, ignore the second sample index, if the second sample index was not used for the 10x sample.
qc	Optional<Boolean>	–qc	Calculate both sequencing and 10x-specific metrics, including per-sample barcode matching rate. Will not be performed unless this flag is specified.
lanes	Optional<Array<String>>	–lanes=	Comma-delimited series of lanes to demultiplex. Shortcut for the –tiles argument.
useBasesMask	Optional<String>	–use-bases-mask=	Same as bcl2fastq; override the read lengths as specified in RunInfo.xml. See Illumina bcl2fastq documentation for more information.
deleteUndetermined	Optional<Boolean>	–delete-undetermined	Delete the Undetermined FASTQ files left by bcl2fastq. Useful if your sample sheet is only expected to match a subset of the flowcell.
project	Optional<String>	–project=	Custom project name, to override the samplesheet or to use in conjunction with the –csv argument.
localcores	Optional<Integer>	–localcores=	Set max cores the pipeline may request at one time. Only applies when –jobmode=local.
localmem	Optional<Float>	–localmem=	Set max GB the pipeline may request at one time. Only applies when –jobmode=local.
nopreflight	Optional<Boolean>	–nopreflight	Skip preflight checks.

Workflow Description Language¶

version development

task CellRangerMkfastq {
  input {
    Int? runtime_cpu
    Int? runtime_memory
    Int? runtime_seconds
    Int? runtime_disks
    Directory run
    String? id
    String? outputFoldername
    File? csv
    File? sampleSheet
    Boolean? ignoreDualIndex
    Boolean? qc
    Array[String]? lanes
    String? useBasesMask
    Boolean? deleteUndetermined
    String? project
    Int? localcores
    Float? localmem
    Boolean? nopreflight
  }
  command <<<
    set -e
    cellranger mkfastq \
      --run='~{run}' \
      ~{if defined(id) then ("--id='" + id + "'") else ""} \
      --output-dir='~{select_first([outputFoldername, "generated"])}' \
      ~{if defined(csv) then ("--csv='" + csv + "'") else ""} \
      ~{if defined(sampleSheet) then ("--sample-sheet='" + sampleSheet + "'") else ""} \
      ~{if (defined(ignoreDualIndex) && select_first([ignoreDualIndex])) then "--ignore-dual-index" else ""} \
      ~{if (defined(qc) && select_first([qc])) then "--qc" else ""} \
      ~{if (defined(lanes) && length(select_first([lanes])) > 0) then "--lanes='" + sep("','", select_first([lanes])) + "'" else ""} \
      ~{if defined(useBasesMask) then ("--use-bases-mask='" + useBasesMask + "'") else ""} \
      ~{if (defined(deleteUndetermined) && select_first([deleteUndetermined])) then "--delete-undetermined" else ""} \
      ~{if defined(project) then ("--project='" + project + "'") else ""} \
      ~{if defined(select_first([localcores, select_first([runtime_cpu, 1])])) then ("--localcores=" + select_first([localcores, select_first([runtime_cpu, 1])])) else ''} \
      ~{if defined(select_first([localmem, select_first([runtime_memory, 4])])) then ("--localmem=" + select_first([localmem, select_first([runtime_memory, 4])])) else ''} \
      ~{if (defined(nopreflight) && select_first([nopreflight])) then "--nopreflight" else ""}
  >>>
  runtime {
    cpu: select_first([runtime_cpu, 1])
    disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
    docker: "fbrundu/cellranger:v3.0.2"
    duration: select_first([runtime_seconds, 86400])
    memory: "~{select_first([runtime_memory, 4])}G"
    preemptible: 2
  }
  output {
    Directory out = select_first([outputFoldername, "generated"])
  }
}

Common Workflow Language¶

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: CellRanger mkfastq
doc: |
  /opt/cellranger-3.0.2/cellranger-cs/3.0.2/bin
  cellranger mkfastq (3.0.2)
  Copyright (c) 2019 10x Genomics, Inc.  All rights reserved.
  -------------------------------------------------------------------------------
  Run Illumina demultiplexer on sample sheets that contain 10x-specific sample
  index sets, and generate 10x-specific quality metrics after the demultiplex.
  Any bcl2fastq argument will work (except a few that are set by the pipeline
  to ensure proper trimming and sample indexing). The FASTQ output generated
  will be the same as when running bcl2fastq directly.
  These bcl2fastq arguments are overridden by this pipeline:
      --fastq-cluster-count
      --minimum-trimmed-read-length
      --mask-short-adapter-reads
  Usage:
      cellranger mkfastq --run=PATH [options]
      cellranger mkfastq -h | --help | --version

requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
  dockerPull: fbrundu/cellranger:v3.0.2

inputs:
- id: run
  label: run
  doc: Path of Illumina BCL run folder.
  type: Directory
  inputBinding:
    prefix: --run=
    separate: false
- id: id
  label: id
  doc: |-
    Name of the folder created by mkfastq. If not supplied, will default to the name of the flowcell referred to by the --run argument.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --id=
    separate: false
- id: outputFoldername
  label: outputFoldername
  doc: Same as in bcl2fastq. Folder where FASTQs, reports and stats will be generated.
  type:
  - string
  - 'null'
  default: generated
  inputBinding:
    prefix: --output-dir=
    separate: false
- id: csv
  label: csv
  doc: |-
    Apparently the same as `sampleSheet`. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet.  Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --csv=
    separate: false
- id: sampleSheet
  label: sampleSheet
  doc: |-
    (--samplesheet= | --csv=) Path to the sample sheet. The sample sheet can either be a simple CSV with lane, sample and index columns, or an Illumina Experiment Manager-compatible sample sheet.  Sample sheet indexes can refer to 10x sample index set names (e.g., SI-GA-A12).
  type:
  - File
  - 'null'
  inputBinding:
    prefix: --sample-sheet=
    separate: false
- id: ignoreDualIndex
  label: ignoreDualIndex
  doc: |-
    On a dual-indexed flowcell, ignore the second sample index, if the second sample index was not used for the 10x sample.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --ignore-dual-index
    separate: true
- id: qc
  label: qc
  doc: |-
    Calculate both sequencing and 10x-specific metrics, including per-sample barcode matching rate. Will not be performed unless this flag is specified.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --qc
    separate: true
- id: lanes
  label: lanes
  doc: |-
    Comma-delimited series of lanes to demultiplex. Shortcut for the --tiles argument.
  type:
  - type: array
    items: string
  - 'null'
  inputBinding:
    prefix: --lanes=
    separate: false
    itemSeparator: ','
- id: useBasesMask
  label: useBasesMask
  doc: |-
    Same as bcl2fastq; override the read lengths as specified in RunInfo.xml. See Illumina bcl2fastq documentation for more information.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --use-bases-mask=
    separate: false
- id: deleteUndetermined
  label: deleteUndetermined
  doc: |-
    Delete the Undetermined FASTQ files left by bcl2fastq.  Useful if your sample sheet is only expected to match a subset of the flowcell.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --delete-undetermined
    separate: true
- id: project
  label: project
  doc: |-
    Custom project name, to override the samplesheet or to use in conjunction with the --csv argument.
  type:
  - string
  - 'null'
  inputBinding:
    prefix: --project=
    separate: false
- id: localcores
  label: localcores
  doc: |-
    Set max cores the pipeline may request at one time. Only applies when --jobmode=local.
  type:
  - int
  - 'null'
  inputBinding:
    prefix: --localcores=
    valueFrom: $([inputs.runtime_cpu, 1].filter(function (inner) { return inner !=
      null })[0])
    separate: false
- id: localmem
  label: localmem
  doc: |-
    Set max GB the pipeline may request at one time. Only applies when --jobmode=local.
  type:
  - float
  - 'null'
  inputBinding:
    prefix: --localmem=
    valueFrom: |-
      $([inputs.runtime_memory, 4].filter(function (inner) { return inner != null })[0])
    separate: false
- id: nopreflight
  label: nopreflight
  doc: Skip preflight checks.
  type:
  - boolean
  - 'null'
  inputBinding:
    prefix: --nopreflight
    separate: true

outputs:
- id: out
  label: out
  type: Directory
  outputBinding:
    glob: generated
    loadContents: false
stdout: _stdout
stderr: _stderr

baseCommand:
- cellranger
- mkfastq
arguments: []

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