ncov2019ArticNf workflow executes the ncov2019-artic-nf Nextflow workflow from connor-lab (https://github.com/connor-lab/ncov2019-artic-nf).
- ncov2019-artic-nf-illumina 20210406
- artic-ncov2019 2
- ncov2019primernames 20201112
- hg38-sars-covid-2 20200714
java -jar cromwell.jar run ncov2019ArticNf.wdl --inputs inputs.json
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. |
Parameter | Value | Default | Description |
---|
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. |
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 |
This section lists command(s) run by ncov2019Artic workflow
- Running ncov2019Artic
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/
For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .
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