bcl2fastq

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

Overview

Dependencies

• bcl2fastq

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 .

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)