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bcl2fastq

Workflow to produce FASTQ files from an Illumina instrument's run directory

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run bcl2fastq.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
lanes Array[Int]+ The lane numbers to process from this run
mismatches Int Number of mismatches to allow in the barcodes (usually, 1)
modules String The modules to load when running the workflow. This should include bcl2fastq and the helper scripts.
samples Array[Sample]+ The information about the samples. Tname of the sample which will determine the output file prefix. The list of barcodes in the format i7-i5 for this sample. If multiple barcodes are provided, they will be merged into a single output.
runDirectory String {'description': "The path to the instrument's output directory.", 'vidarr_type': 'directory'}

Optional workflow parameters:

Parameter Value Default Description
basesMask String? None An Illumina bases mask string to use. If absent, the one written by the instrument will be used.
timeout Int 40 The maximum number of hours this workflow can run for.

Optional task parameters:

Parameter Value Default Description
process.bcl2fastq String "bcl2fastq" The name or path of the BCL2FASTQ executable.
process.bcl2fastqJail String "bcl2fastq-jail" The name ro path of the BCL2FASTQ wrapper script executable.
process.extraOptions String "" Any other options that will be passed directly to bcl2fastq.
process.ignoreMissingBcls Boolean false Flag passed to bcl2fastq, allows missing bcl files.
process.ignoreMissingFilter Boolean false Flag passed to bcl2fastq, allows missing or corrupt filter files.
process.ignoreMissingPositions Boolean false Flag passed to bcl2fastq, allows missing or corrupt positions files.
process.memory Int 32 The memory for the BCL2FASTQ process in GB.
process.temporaryDirectory String "." A directory where bcl2fastq can dump massive amounts of garbage while running.
process.threads Int 8 The number of processing threads to use when running BCL2FASTQ

Outputs

Output Type Description
fastqs Array[Output]+ A list of FASTQs generated and annotations that should be applied to them.

Commands

This section lists command(s) run by bcl2fastq workflow

  • Running bcl2fastq

Convert basecalls to fastq

    BCL2FASTQ_JAIL 
      -t TMP_DIR 
      -s SAMPLES_JSON 
      -- BCL2FASTQ 
      --barcode-mismatches MISMATCHES 
      --input-dir INPUT_DIR 
      --intensities-dir RUN_DIR/Data/Intensities 
      --no-lane-splitting 
      --processing-threads THREADS 
      --runfolder-dir RUN_DIR 
      --tiles TITLES 
      --interop-dir TMP_DIR 
      
      Optional Parameters:

      --ignore-missing-bcls 
      --ignore-missing-filter 
      --ignore-missing-positions
      --use-bases-mask CUSTOM_BASE_MASK 
        EXTRA_OPTIONS

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

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