sarsCoV2Analysis

Classify samples as being either SARS-CoV-2 positive or negative, identify the strain of virus, and produce statistics about the mapping.

Overview

Dependencies

• bbmap 38.75
• bowtie2 2.3.5.1
• samtools 1.9
• kraken2 2.0.8
• ivar 1.0
• bcftools 1.9
• vcftools 0.1.16
• seqtk 1.3
• bedtools 2.27
• blast 2.8.1
• spades 3.14.0

Usage

Cromwell

java -jar cromwell.jar run sarsCoV2Analysis.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
fastq1	File	Read 1 fastq file, gzipped. Can be either targeted or whole transcriptome
fastq2	File	Read 2 fastq file, gzipped. Can be either targeted or whole transcriptome.
samplePrefix	String	Prefix for output files

Optional workflow parameters:

Parameter	Value	Default	Description
primerBed	File?	None	Bed file used to trim the primers off of the bam sequences.
panelBed	File?	None
readCount	Int?	None	Number of reads for fastq files.

Optional task parameters:

Parameter	Value	Default	Description
bbMap.modules	String	"bbmap/38.75"
bbMap.reference	String	"$BBMAP_ROOT/share/bbmap/resources/adapters.fa"
bbMap.trimq	Int	25
bbMap.mem	Int	8
bbMap.timeout	Int	72
bowtie2HumanDepletion.modules	String	"bowtie2/2.3.5.1 samtools/1.9 hg38-bowtie-index/2.3.5.1"
bowtie2HumanDepletion.reference	String	"$HG38_BOWTIE_INDEX_ROOT/hg38_random_index"
bowtie2HumanDepletion.mem	Int	12
bowtie2HumanDepletion.timeout	Int	72
bowtie2HumanDepletion.threads	Int	8
kraken2.modules	String	"kraken2/2.0.8 kraken2-database/1"
kraken2.kraken2DB	String	"$KRAKEN2_DATABASE_ROOT/"
kraken2.mem	Int	8
kraken2.timeout	Int	72
bowtie2Sensitive.modules	String	"bowtie2/2.3.5.1 sars-covid-2-polymasked-bowtie-index/2.3.5.1 samtools/1.9"
bowtie2Sensitive.sarsCovidIndex	String	"$SARS_COVID_2_POLYMASKED_BOWTIE_INDEX_ROOT/MN908947.3.mask"
bowtie2Sensitive.mem	Int	8
bowtie2Sensitive.timeout	Int	72
bowtie2Sensitive.threads	Int	4
articTrimming.allowNoprimer	Boolean?	None	Allow reads that don't have primer sequence? Ligation prep = false, nextera = true.
articTrimming.bam	File	None	Host depleted and aligned to mn908947 bam file.
articTrimming.modules	String	"ivar/1.0 bedtools"	Environment module name and version to load (space separated) before command execution.
articTrimming.mem	Int	8	Memory (in GB) to allocate to the job.
articTrimming.timeout	Int	72	Maximum amount of time (in hours) the task can run for.
variantCalling.modules	String	"bcftools/1.9 samtools/1.9 vcftools/0.1.16 seqtk/1.3 sars-covid-2-polymasked/mn908947.3"
variantCalling.sarsCovidRef	String	"$SARS_COVID_2_POLYMASKED_ROOT/MN908947.3.mask.fasta"
variantCalling.mem	Int	8
variantCalling.timeout	Int	72
qcStats.modules	String	"bedtools samtools/1.9"
qcStats.mem	Int	8
qcStats.timeout	Int	72
blast2ReferenceSequence.modules	String	"blast sars-covid-2-polymasked/mn908947.3"
blast2ReferenceSequence.reference	String	"$SARS_COVID_2_POLYMASKED_ROOT/MN908947.3.mask.fasta"
blast2ReferenceSequence.mem	Int	8
blast2ReferenceSequence.timeout	Int	72
spadesGenomicAssembly.modules	String	"spades/3.14.0"
spadesGenomicAssembly.mem	Int	8
spadesGenomicAssembly.timeout	Int	72
spadesGenomicAssembly.minReads	Int	100

Outputs

Output	Type	Description
hostRemovedR1Fastq	File	None
hostRemovedR2Fastq	File	None
hostMappedBam	File	None
hostMappedBai	File	None
taxonomicClassification	File	None
bam	File	None
bai	File	None
primertrimSortedBam	File?	None
primertrimSortedBai	File?	None
cvgHist	File?	None
vcf	File	None
consensusFasta	File	None
variantOnlyVcf	File	None
bl2seqReport	File	None
genomecvgHist	File	None
genomecvgPerBase	File	None
hostMappedAlignmentStats	File	None
hostDepletedAlignmentStats	File	None
spades	File	None

Niassa + Cromwell

This WDL workflow is wrapped in a Niassa workflow (https://github.com/oicr-gsi/pipedev/tree/master/pipedev-niassa-cromwell-workflow) so that it can used with the Niassa metadata tracking system (https://github.com/oicr-gsi/niassa).

• Building

mvn clean install

• Testing

mvn clean verify \
-Djava_opts="-Xmx1g -XX:+UseG1GC -XX:+UseStringDeduplication" \
-DrunTestThreads=2 \
-DskipITs=false \
-DskipRunITs=false \
-DworkingDirectory=/path/to/tmp/ \
-DschedulingHost=niassa_oozie_host \
-DwebserviceUrl=http://niassa-url:8080 \
-DwebserviceUser=niassa_user \
-DwebservicePassword=niassa_user_password \
-Dcromwell-host=http://cromwell-url:8000

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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