ncov2019ArticNf

ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run ncov2019ArticNf.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
`fastqR1`	File	Read 1 fastq file.
`fastqR2`	File	Read 2 fastq file.
`outputFileNamePrefix`	String	Output prefix to prefix output file names with.
`schemeVersion`	String	The Artic primer scheme version that was used.

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
`renameInputs.mem`	Int	1	Memory (in GB) to allocate to the job.
`renameInputs.timeout`	Int	1	Maximum amount of time (in hours) the task can run for.
`illumina_ncov2019ArticNf.viralContigName`	String	"MN908947.3"	Viral contig name to retain during non-human filtering step.
`illumina_ncov2019ArticNf.allowNoprimer`	Boolean?	None	Allow reads that don't have primer sequence? Ligation prep = false, nextera = true.
`illumina_ncov2019ArticNf.illuminaKeepLen`	Int?	None	Length of illumina reads to keep after primer trimming.
`illumina_ncov2019ArticNf.illuminaQualThreshold`	Int?	None	Sliding window quality threshold for keeping reads after primer trimming (illumina).
`illumina_ncov2019ArticNf.mpileupDepth`	Int?	None	Mpileup depth for ivar.
`illumina_ncov2019ArticNf.ivarFreqThreshold`	Float?	None	ivar frequency threshold for variant.
`illumina_ncov2019ArticNf.ivarMinDepth`	Float?	None	Minimum coverage depth to call variant.
`illumina_ncov2019ArticNf.additionalParameters`	String?	None	Additional parameters to add to the nextflow command.
`illumina_ncov2019ArticNf.mem`	Int	8	Memory (in GB) to allocate to the job.
`illumina_ncov2019ArticNf.timeout`	Int	5	Maximum amount of time (in hours) the task can run for.
`illumina_ncov2019ArticNf.modules`	String	"ncov2019-artic-nf-illumina/20210406 artic-ncov2019/2 ncov2019primernames/20201112 hg38-sars-covid-2/20200714"	Environment module name and version to load (space separated) before command execution.
`illumina_ncov2019ArticNf.ncov2019ArticNextflowPath`	String	"$NCOV2019_ARTIC_NF_ILLUMINA_ROOT"	Path to the ncov2019-artic-nf-illumina repository directory.
`illumina_ncov2019ArticNf.ncov2019ArticPath`	String	"$ARTIC_NCOV2019_ROOT"	Path to the artic-ncov2019 repository directory or url
`illumina_ncov2019ArticNf.compositeHumanVirusReferencePath`	String	"$HG38_SARS_COVID_2_ROOT/composite_human_virus_reference.fasta"	Path to the composite reference to use during non-human filtering step.
`illumina_ncov2019ArticNf.ncov2019primerNames`	String	"$NCOV2019PRIMERNAMES_ROOT/nCoV-2019.outer.V3.primernames.tsv"	Path to primer names for improved primer trimming.

Outputs

Output	Type	Description	Labels
`readTrimmingFastqR1`	File	Fastq R1 from readTrimming step.	vidarr_label: readTrimmingFastqR1
`readTrimmingFastqR2`	File	Fastq R1 from readTrimming step.	vidarr_label: readTrimmingFastqR2
`readMappingBam`	File	Sorted bam from readMapping step.	vidarr_label: readMappingBam
`trimPrimerSequencesBam`	File	Mapped bam from trimPrimerSequences step.	vidarr_label: trimPrimerSequencesBam
`trimPrimerSequencesPrimerTrimmedBam`	File	Mapped + primer trimmer bam from trimPrimerSequences step.	vidarr_label: trimPrimerSequencesPrimerTrimmedBam
`makeConsensusFasta`	File	Consensus fasta from makeConsensus step.	vidarr_label: makeConsensusFasta
`makeConsensusVcf`	File	Consensus vcf from makeConsensus step.	vidarr_label: makeConsensusVcf
`qcPlotsPng`	File	Qc plot (depth) png from qcPlots step.	vidarr_label: qcPlotsPng
`qcCsv`	File	Qc csv from qc step.	vidarr_label: qcCsv
`nextflowLogs`	File	All nextflow workflow task stdout and stderr logs gzipped and named by task.	vidarr_label: nextflowLogs

Commands

This section lists command(s) run by ncov2019Artic workflow

Running ncov2019Artic

Linking fastq files

    ln -s ~{fastqR1} ~{outputFileNamePrefix}_R1.fastq.gz
    ln -s ~{fastqR2} ~{outputFileNamePrefix}_R2.fastq.gz

Running workflow as Nextflow wf

    set -euo pipefail

    nextflow run ~{ncov2019ArticNextflowPath} \
    --illumina \
    --directory "$(dirname ~{fastqR1})" \
    --prefix "~{outputFileNamePrefix}" \
    --schemeRepoURL ~{ncov2019ArticPath} \
    --schemeVersion ~{schemeVersion} \
    ~{true="--allowNoprimer true" false="--allowNoprimer false" allowNoprimer} \
    ~{"--illuminaKeepLen " + illuminaKeepLen} \
    ~{"--illuminaQualThreshold " + illuminaQualThreshold} \
    ~{"--mpileupDepth " + mpileupDepth} \
    ~{"--ivarFreqThreshold " + ivarFreqThreshold} \
    ~{"--ivarMinDepth " + ivarMinDepth} \
    --composite_ref ~{compositeHumanVirusReferencePath} \
    --viral_contig_name ~{viralContigName} \
    --primer_pairs_tsv ~{ncov2019primerNames} \
    ~{additionalParameters}

    # rename some of the outputs
    ln -s "results/ncovIllumina_sequenceAnalysis_readTrimming/~{outputFileNamePrefix}_hostfiltered_R1_val_1.fq.gz" \
    ~{outputFileNamePrefix}_R1.trimmed.fastq.gz
    ln -s "results/ncovIllumina_sequenceAnalysis_readTrimming/~{outputFileNamePrefix}_hostfiltered_R2_val_2.fq.gz" \
    ~{outputFileNamePrefix}_R2.trimmed.fastq.gz

    # extract all logs from the nextflow working directory
    NEXTFLOW_ID="$(nextflow log -q | head -1)"
    NEXTFLOW_TASKS=$(nextflow log "${NEXTFLOW_ID}" -f "name,workdir" -s '\t')
    mkdir -p logs
    while IFS=$'\t' read -r name workdir; do
      FILENAME="$(echo "${name}" | sed -e 's/[^A-Za-z0-9._-]/_/g')"
      if [ -f "$workdir/.command.log" ]; then
        cp "$workdir/.command.log" "logs/$FILENAME.stdout"
      fi
      if [ -f "$workdir/.command.err" ]; then
        cp "$workdir/.command.err" "logs/$FILENAME.stderr"
      fi
    done <<< ${NEXTFLOW_TASKS}
    tar -zcvf ~{outputFileNamePrefix}.logs.tar.gz logs/

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 / ncov2019ArticNf