bcl2barcode

bcl2barcode produces index (barcode) counts for all reads in a lane or set of lanes.

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run bcl2barcode.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'}
`lanes`	Array[Int]	A single lane or a list of lanes for no lane splitting (merging lanes).
`basesMask`	String	The bases mask to produce the index reads (e.g. single 8bp index = "Y1N,I8,N", dual 8bp index = "Y1N,I8,I8,N").

Optional workflow parameters:

Parameter	Value	Default	Description
`outputFileNamePrefix`	String?	None	Output prefix to prefix output file names with.

Optional task parameters:

Parameter	Value	Default	Description
`generateIndexFastqs.bcl2fastq`	String	"bcl2fastq"	bcl2fastq binary name or path to bcl2fastq.
`generateIndexFastqs.modules`	String	"bcl2fastq/2.20.0.422"	Environment module name and version to load (space separated) before command execution.
`generateIndexFastqs.mem`	Int	32	Memory (in GB) to allocate to the job.
`generateIndexFastqs.timeout`	Int	6	Maximum amount of time (in hours) the task can run for.
`countDualIndex.bgzip`	String	"bgzip"	bgzip binary name or path to bgzip.
`countDualIndex.modules`	String	"htslib/1.9"	Environment module name and version to load (space separated) before command execution.
`countDualIndex.mem`	Int	16	Memory (in GB) to allocate to the job.
`countDualIndex.cores`	Int	16	The number of cores to allocate to the job.
`countDualIndex.timeout`	Int	6	Maximum amount of time (in hours) the task can run for.
`countSingleIndex.bgzip`	String	"bgzip"	bgzip binary name or path to bgzip.
`countSingleIndex.modules`	String	"htslib/1.9"	Environment module name and version to load (space separated) before command execution.
`countSingleIndex.mem`	Int	16	Memory (in GB) to allocate to the job.
`countSingleIndex.cores`	Int	16	The number of cores to allocate to the job.
`countSingleIndex.timeout`	Int	6	Maximum amount of time (in hours) the task can run for.

Outputs

Output	Type	Description	Labels
`counts`	File	Gzipped and sorted index counts in csv format (count,index).	vidarr_label: counts

Commands

This section lists command(s) run by bcl2barcode workflow

Running bcl2barcode

Generate index fastq file(s)

     BCL2FASTQ \
     --runfolder-dir RUN_DIRECTORY \
     --intensities-dir RUN_DIRECTORY/Data/Intensities/ \
     --processing-threads 8 \
     --output-dir OUTPUT_DIRECTORY \
     --create-fastq-for-index-reads \
     --sample-sheet /dev/null \
     --tiles s_LANES \
     --use-bases-mask BASES_MASK \
     --no-lane-splitting \
     --interop-dir OUTPUT_DIRECTORY/Interop

Output Gzipped and sorted index counts in csv format, for a single index run

     BGZIP_FILE -@ CORES -cd FASTQ_INDEX1 | \
     awk 'NR%4==2' | \
     awk COUNTS
 
     END {for (i in COUNTS) {print COUNTS[i] "," i}}' | \
     sort -nr | \
     gzip -n > [OUTPUT_FILE_NAME_PREFIX]counts.gz

Output Gzipped and sorted index counts in csv format, for a dual index run

     paste -d '-' \
     <(BGZIP_FILE -@ HALF_CORES_ROUNDED_UP -cd FASTQ_INDEX1 | awk 'NR%4==2') \
     <(BGZIP_FILE -@ HALF_CORES_ROUNDED_DOWN -cd FASTQ_INDEX2 | awk 'NR%4==2') | \
     awk COUNTS
 
     END {for (i in COUNTS) {print COUNTS[i] "," i}}' | \
     sort -nr | \
     gzip -n > [OUTPUT_FILE_NAME_PREFIX]counts.gz"

Support

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

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oicr-gsi / bcl2barcode