bclconvert

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

Overview

Dependencies

• bclconvert
• bclconvert-scripts

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
runDirectory	String	{'description': 'Illumina run directory (e.g. /path/to/191219_M00000_0001_000000000-ABCDE).', 'vidarr_type': 'directory'}
mode	String	Either dragen or hpc, selected mode will determined the backend used to run all this
sampleName	String	Sample (we accept only one)
barcodes	Array[String]+	Array of barcode(s)

Optional workflow parameters:

Parameter	Value	Default	Description
lanes	Array[Int]	[]	Extract reads only for specified lanes
basesMask	String?	None	An Illumina bases mask string to use. If absent, the one written by the instrument will be used.
mismatches	Int	1	Number of mismatches to allow in the barcodes (usually, 1)

Optional task parameters:

Parameter	Value	Default	Description
buildSamplesheet.modules	String	"bclconvert-scripts/1.1"	Modules for running bclconvert task
buildSamplesheet.samplesheetScript	String	"$BCLCONVERT_SCRIPTS_ROOT/bin/buildSamplesheet.py"	Script for generating sample sheet
buildSamplesheet.memory	Int	4	Memory allocated for running this task
buildSamplesheet.timeout	Int	2	Timeout for building a samplesheet
runBclconvertHpc.runName	String	basename(runFolder)	Run name
runBclconvertHpc.firstTileOnly	Boolean	false	Flag for processing first tile only
runBclconvertHpc.noLaneSplitting	Boolean	false	Flag to disable lane splitting
runBclconvertHpc.fastqCompression	String	'gzip'	Compression type of fastq files
runBclconvertHpc.fastqCompressionLevel	Int	1	Fastq compression level
runBclconvertHpc.timeout	Int	40	Timeout for this task
runBclconvertHpc.memory	Int	32	Memory allocated for running this task
runBclconvertHpc.modules	String	"bclconvert/4.2.7-2"	Modules for running bclconvert task
runBclconvertHpc.additionalParameters	String?	None	Pass parameters which were not exposed
runBclconvertDragen.runName	String	basename(runFolder)	Run name
runBclconvertDragen.firstTileOnly	Boolean	false	Flag for processing first tile only
runBclconvertDragen.noLaneSplitting	Boolean	false	Flag to disable lane splitting
runBclconvertDragen.fastqCompression	String	'gzip'	Compression type of fastq files
runBclconvertDragen.fastqCompressionLevel	Int	1	Fastq compression level
runBclconvertDragen.timeout	Int	40	Timeout for this task
runBclconvertDragen.additionalParameters	String?	None	Pass parameters which were not exposed
postprocessResults.runName	String	basename(runFolder)	Run name
postprocessResults.modules	String	"bclconvert-scripts/1.1"	Module with python bclconvert scripts
postprocessResults.bclconvertScript	String	"$BCLCONVERT_SCRIPTS_ROOT/bin/runBclconvert.py"	Script for generating sample sheet
postprocessResults.timeout	Int	12	Timeout for this task
postprocessResults.memory	Int	8	Memory allocated for running this task

Outputs

Output	Type	Description	Labels
fastq_read1	Pair[File,Map[String,String]]	FASTQ reads 1st in pair.
fastq_read2	Pair[File,Map[String,String]]?	FASTQ reads 2nd in pair.

Commands

This section lists commands run by bclconvert workflow

• Running bclconvert

Create a samplesheet

This step creates a csv file with sample and barcode information. Required for bclconvert task

   python3 ~{samplesheetScript} -i "~{write_json(sample)}" -m "~{basesMask}" -l "~{sep=',' lanes}"

Run bclconvert in HPC mode

Run Illumina's bclconvert to produce fastq files

   set -euo pipefail
   bcl-convert -f \
   --bcl-input-directory ~{runFolder} \
   --output-directory . \
   --sample-sheet ~{sampleSheet} \
   --no-lane-splitting ~{noLaneSplitting} \
   --first-tile-only ~{firstTileOnly} \
   --bcl-only-matched-reads true \
   --fastq-gzip-compression-level ~{fastqCompressionLevel} ~{additionalParameters}
   
   zip ~{runName}.reports.gz Reports/*

Run bclconvert in DRAGEN mode

   set -euo pipefail
   dragen -f --bcl-conversion-only true \
   --bcl-input-directory ~{runFolder} \
   --output-directory . \
   --sample-sheet ~{sampleSheet} \
   --no-lane-splitting ~{noLaneSplitting} \
   --first-tile-only ~{firstTileOnly} \
   --bcl-only-matched-reads true \
   --fastq-compression-format ~{fastqCompression} \
   --fastq-gzip-compression-level ~{fastqCompressionLevel} ~{additionalParameters}
 
   zip ~{runName}.reports.gz Reports/*

Post-process files

Rename files using library id, sequencing run, lane and barcode. Assemble additional metadata into an object for the final output

  python3 ~{bclconvertScript} -r ~{runName} -d ~{demultiplexStats} -l ~{fastqList} -f ~{sep="," fastqs}

Support

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

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