Viralrecon - Bioinformatics analysis pipeline for low-frequency variant calling.

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nf-core-viralrecon
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nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intrahost/low-frequency variant calling for viral samples. The pipeline currently supports metagenomics and amplicon sequencing data derived from the Illumina sequencing platform.

This pipeline is a re-implementation of the SARS_Cov2_consensus-nf and SARS_Cov2_assembly-nf pipelines initially developed by Sarai Varona and Sara Monzon from BU-ISCIII . Porting both of these pipelines to nf-core was an international collaboration between numerous contributors and developers, led by Harshil Patel from the The Bioinformatics & Biostatistics Group at The Francis Crick Institute , London. We appreciated the need to have a portable, reproducible and scalable pipeline for the analysis of COVID-19 sequencing samples and so the Avengers Assembled! Please come and join us and add yourself to the contributor list :)

We have integrated a number of options in the pipeline to allow you to run specific aspects of the workflow if you so wish. For example, you can skip all of the assembly steps with the --skip_assembly parameter. See usage docs for all of the available options when running the pipeline.

Pipeline summary

  1. Download samples via SRA, ENA or GEO ids ( ENA FTP , parallel-fastq-dump ; if required )
  2. Merge re-sequenced FastQ files ( cat ; if required )
  3. Read QC ( FastQC )
  4. Adapter trimming ( fastp )
  5. Variant calling
    i. Read alignment ( Bowtie 2 )
    ii. Sort and index alignments ( SAMtools )
    iii. Primer sequence removal ( iVar ; amplicon data only )
    iv. Duplicate read marking ( picard ; removal optional )
    v. Alignment-level QC ( picard , SAMtools )
    vi. Choice of multiple variant calling and consensus sequence generation routes ( VarScan 2 , BCFTools , BEDTools || iVar variants and consensus || BCFTools , BEDTools )
    - Variant annotation ( SnpEff , SnpSift )
    - Consensus assessment report ( QUAST )
  6. De novo assembly
    i. Primer trimming ( Cutadapt ; amplicon data only )
    ii. Removal of host reads ( Kraken 2 )
    iii. Choice of multiple assembly tools ( SPAdes || metaSPAdes || Unicycler || minia )
    - Blast to reference genome ( blastn )
    - Contiguate assembly ( ABACAS )
    - Assembly report ( PlasmidID )
    - Assembly assessment report ( QUAST )
    - Call variants relative to reference ( Minimap2 , seqwish , vg , Bandage )
    - Variant annotation ( SnpEff , SnpSift )
  7. Present QC and visualisation for raw read, alignment, assembly and variant calling results ( MultiQC )

Code Snippets

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"""
zcat $vcf \\
    | grep -v '#' \\
    | awk -v FS='\t' -v OFS='\t' '{print \$1, (\$2-1), (\$2)}' \\
    > variants.bed

bedtools \\
    slop \\
    -i variants.bed \\
    -g $sizes \\
    -b $window \\
    > variants.slop.bed

ASCIIGenome \\
    -ni \\
    -x "trackHeight 0 bam#1 && trackHeight $track_height bam@2 $paired_end && filterVariantReads && save ${prefix}.%r.pdf" \\
    --batchFile variants.slop.bed \\
    --fasta $fasta \\
    $bam \\
    $vcf \\
    $bed_track \\
    $gff_track \\
    > /dev/null

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    asciigenome: \$(echo \$(ASCIIGenome -ni --version 2>&1) | sed -e "s/ASCIIGenome //g")
    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
NextFlow BEDTools asciigenome From line 31 of local/asciigenome.nf 
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"""
collapse_primer_bed.py \\
    --left_primer_suffix $left_suffix \\
    --right_primer_suffix $right_suffix \\
    $bed \\
    ${bed.baseName}.collapsed.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 23 of local/collapse_primers.nf 
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"""
sed -r '/^[ACTGactg]+\$/ s/\$/X/g' $adapters > adapters.sub.fa

cutadapt \\
    --cores $task.cpus \\
    $args \\
    $paired \\
    $trimmed \\
    $reads \\
    > ${prefix}.cutadapt.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cutadapt: \$(cutadapt --version)
END_VERSIONS
"""
NextFlow Cutadapt From line 27 of local/cutadapt.nf 
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"""
awk 'BEGIN{OFS=\"\\t\";FS=\"\\t\"}{print \$0,\$5/\$15,\$5/\$14}' $hits | awk 'BEGIN{OFS=\"\\t\";FS=\"\\t\"} \$15 > 200 && \$17 > 0.7 && \$1 !~ /phage/ {print \$0}' > tmp.out
cat $header tmp.out > ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 23 of local/filter_blastn.nf 
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"""
ivar_variants_to_vcf.py \\
    $tsv \\
    ${prefix}.vcf \\
    --fasta $fasta \\
    $args \\
    > ${prefix}.variant_counts.log

cat $header ${prefix}.variant_counts.log > ${prefix}.variant_counts_mqc.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 26 of local/ivar_variants_to_vcf.nf 
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"""
kraken2-build --db kraken2_db --threads $task.cpus $args  --download-taxonomy
kraken2-build --db kraken2_db --threads $task.cpus $args2 --download-library $library
kraken2-build --db kraken2_db --threads $task.cpus $args3 --build

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
    pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
NextFlow kraken2 From line 24 of local/kraken2_build.nf 
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"""
samtools \\
    mpileup \\
    $args \\
    --reference $fasta \\
    $bam \\
    $mpileup  \\
    | awk -v OFS='\\t' '{print \$1, \$2-1, \$2, \$4}' | awk '\$4 < $args2' > lowcov_positions.txt

make_bed_mask.py \\
    $vcf \\
    lowcov_positions.txt \\
    ${prefix}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow SAMtools From line 27 of local/make_bed_mask.nf 
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"""
make_variants_long_table.py \\
    --bcftools_query_dir ./bcftools_query \\
    --snpsift_dir ./snpsift \\
    --pangolin_dir ./pangolin \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow Pangolin From line 22 of local/make_variants_long_table.nf 
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"""
## Run MultiQC once to parse tool logs
multiqc -f $args $custom_config .

## Parse YAML files dumped by MultiQC to obtain metrics
multiqc_to_custom_csv.py --platform illumina

## Manually remove files that we don't want in the report
if grep -q ">skip_assembly<" workflow_summary_mqc.yaml; then
    rm -f *assembly_metrics_mqc.csv
fi

if grep -q ">skip_variants<" workflow_summary_mqc.yaml; then
    rm -f *variants_metrics_mqc.csv
fi

rm -f variants/report.tsv

## Run MultiQC a second time
multiqc -f $args -e general_stats --ignore nextclade_clade_mqc.tsv $custom_config .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
NextFlow MultiQC From line 50 of local/multiqc_illumina.nf 
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"""
## Run MultiQC once to parse tool logs
multiqc -f $args $custom_config .

## Parse YAML files dumped by MultiQC to obtain metrics
multiqc_to_custom_csv.py --platform nanopore

## Manually remove files that we don't want in the report
rm -rf quast

## Run MultiQC a second time
multiqc -f $args -e general_stats --ignore *nextclade_clade_mqc.tsv $custom_config .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
NextFlow MultiQC QUAST From line 42 of local/multiqc_nanopore.nf 
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"""
plot_base_density.r \\
    --fasta_files $fasta \\
    --prefixes $prefix \\
    --output_dir ./

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 23 of local/plot_base_density.nf 
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"""
plot_mosdepth_regions.r \\
    --input_files ${beds.join(',')} \\
    --output_dir ./ \\
    --output_suffix $prefix \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 25 of local/plot_mosdepth_regions.nf 
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"""
sed "s/>/>${meta.id} /g" $fasta > ${prefix}.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sed: \$(echo \$(sed --version 2>&1) | sed 's/^.*GNU sed) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 21 of local/rename_fasta_header.nf 
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"""
check_samplesheet.py \\
    $samplesheet \\
    samplesheet.valid.csv \\
    --platform $platform

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 22 of local/samplesheet_check.nf 
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"""
snpEff \\
    -Xmx${avail_mem}g \\
    ${fasta.baseName} \\
    -config $config \\
    -dataDir $db \\
    $args \\
    $vcf \\
    -csvStats ${prefix}.snpeff.csv \\
    > ${prefix}.snpeff.vcf
mv snpEff_summary.html ${prefix}.snpeff.summary.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS
"""
NextFlow snpEff From line 36 of local/snpeff_ann.nf 
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"""
mkdir -p snpeff_db/genomes/
cd snpeff_db/genomes/
ln -s ../../$fasta ${basename}.fa

cd ../../
mkdir -p snpeff_db/${basename}/
cd snpeff_db/${basename}/
ln -s ../../$gff genes.gff

cd ../../
echo "${basename}.genome : ${basename}" > snpeff.config

snpEff \\
    -Xmx${avail_mem}g \\
    build \\
    -config snpeff.config \\
    -dataDir ./snpeff_db \\
    -gff3 \\
    -v \\
    ${basename}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    snpeff: \$(echo \$(snpEff -version 2>&1) | cut -f 2 -d ' ')
END_VERSIONS
"""
NextFlow snpEff From line 31 of local/snpeff_build.nf 
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"""
SnpSift \\
    -Xmx${avail_mem}g \\
    extractFields \\
    -s "," \\
    -e "." \\
    $args \\
    $vcf \\
    CHROM POS REF ALT \\
    "ANN[*].GENE" "ANN[*].GENEID" \\
    "ANN[*].IMPACT" "ANN[*].EFFECT" \\
    "ANN[*].FEATURE" "ANN[*].FEATUREID" \\
    "ANN[*].BIOTYPE" "ANN[*].RANK" "ANN[*].HGVS_C" \\
    "ANN[*].HGVS_P" "ANN[*].CDNA_POS" "ANN[*].CDNA_LEN" \\
    "ANN[*].CDS_POS" "ANN[*].CDS_LEN" "ANN[*].AA_POS" \\
    "ANN[*].AA_LEN" "ANN[*].DISTANCE" "EFF[*].EFFECT" \\
    "EFF[*].FUNCLASS" "EFF[*].CODON" "EFF[*].AA" "EFF[*].AA_LEN" \\
    > ${prefix}.snpsift.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
END_VERSIONS
"""
NextFlow SnpSift From line 30 of local/snpsift_extractfields.nf 
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"""
abacas.pl \\
    -r $fasta \\
    -q $scaffold \\
    $args \\
    -o ${prefix}.abacas

mv nucmer.delta ${prefix}.abacas.nucmer.delta
mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    abacas: \$(echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//')
END_VERSIONS
"""
NextFlow assembly_improvement From line 24 of abacas/main.nf 
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"""
artic \\
    guppyplex \\
    $args \\
    --directory $fastq_dir \\
    --output ${prefix}.fastq

pigz -p $task.cpus *.fastq
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    artic: $VERSION
END_VERSIONS
"""
NextFlow artic From line 24 of guppyplex/main.nf 
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"""
$hd5_plugin_path

artic \\
    minion \\
    $args \\
    --threads $task.cpus \\
    --read-file $fastq \\
    --scheme-directory ./primer-schemes \\
    --scheme-version $version \\
    $model \\
    $fast5 \\
    $summary \\
    $scheme \\
    $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    artic: $VERSION
END_VERSIONS
"""
NextFlow artic From line 52 of minion/main.nf 
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"""
Bandage image $gfa ${prefix}.png $args
Bandage image $gfa ${prefix}.svg $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bandage: \$(echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow Bandage From line 24 of image/main.nf 
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"""
cat $fasta \\
    | bcftools \\
        consensus \\
        $vcf \\
        $args \\
        > ${prefix}.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools Consensus From line 23 of consensus/main.nf 
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"""
bcftools filter \\
    --output ${prefix}.vcf.gz \\
    $args \\
    $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 23 of filter/main.nf 
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"""
touch ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 38 of filter/main.nf 
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"""
echo "${meta.id}" > sample_name.list

bcftools \\
    mpileup \\
    --fasta-ref $fasta \\
    $args \\
    $bam \\
    $intervals \\
    $mpileup \\
    | bcftools call --output-type v $args2 \\
    | bcftools reheader --samples sample_name.list \\
    | bcftools view --output-file ${prefix}.vcf.gz --output-type z $args3

$bgzip_mpileup

tabix -p vcf -f ${prefix}.vcf.gz

bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools tabix From line 33 of mpileup/main.nf 
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"""
bcftools norm \\
    --fasta-ref ${fasta} \\
    --output ${prefix}.${extension}\\
    $args \\
    --threads $task.cpus \\
    ${vcf}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 30 of norm/main.nf 
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"""
touch ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 52 of norm/main.nf 
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"""
bcftools query \\
    --output ${prefix}.txt \\
    $regions_file \\
    $targets_file \\
    $samples_file \\
    $args \\
    $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 29 of query/main.nf 
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"""
bcftools \\
    sort \\
    --output ${prefix}.${extension} \\
    $args \\
    $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 29 of sort/main.nf 
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"""
touch ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 52 of sort/main.nf 
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"""
bcftools stats \\
    $args \\
    $regions_file \\
    $targets_file \\
    $samples_file \\
    $vcf > ${prefix}.bcftools_stats.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 29 of stats/main.nf 
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"""
touch ${prefix}.bcftools_stats.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 46 of stats/main.nf 
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"""
bedtools \\
    getfasta \\
    $args \\
    -fi $fasta \\
    -bed $bed \\
    -fo ${prefix}.fa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
NextFlow BEDTools From line 24 of getfasta/main.nf 
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"""
bedtools \\
    maskfasta \\
    $args \\
    -fi $fasta \\
    -bed $bed \\
    -fo ${prefix}.fa
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
NextFlow BEDTools From line 24 of maskfasta/main.nf 
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"""
bedtools \\
    merge \\
    -i $bed \\
    $args \\
    > ${prefix}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
END_VERSIONS
"""
NextFlow BEDTools From line 24 of merge/main.nf 
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"""
DB=`find -L ./ -name "*.ndb" | sed 's/\\.ndb\$//'`
blastn \\
    -num_threads $task.cpus \\
    -db \$DB \\
    -query $fasta \\
    $args \\
    -out ${prefix}.blastn.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BLAST From line 24 of blastn/main.nf 
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"""
makeblastdb \\
    -in $fasta \\
    $args
mkdir blast_db
mv ${fasta}* blast_db
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    blast: \$(blastn -version 2>&1 | sed 's/^.*blastn: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 22 of makeblastdb/main.nf 
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"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1

bowtie2 \\
    -x \$INDEX \\
    $reads_args \\
    --threads $task.cpus \\
    $unaligned \\
    $args \\
    2> ${prefix}.bowtie2.log \\
    | samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -

if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
    mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
fi

if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
    mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
    pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
NextFlow SAMtools Bowtie 2 From line 42 of align/main.nf 
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"""
mkdir bowtie2
bowtie2-build $args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bowtie2: \$(echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow Bowtie 2 From line 22 of build/main.nf 
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"""
cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 26 of fastq/main.nf 
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"""
cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 40 of fastq/main.nf 
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"""
touch ${prefix}.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 57 of fastq/main.nf 
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"""
touch ${prefix}_1.merged.fastq.gz
touch ${prefix}_2.merged.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 68 of fastq/main.nf 
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"""
samtools faidx $fasta
cut -f 1,2 ${fasta}.fai > ${fasta}.sizes

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of getchromsizes/main.nf 
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"""
touch ${fasta}.fai
touch ${fasta}.sizes

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    getchromsizes: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 35 of getchromsizes/main.nf 
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"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --stdout \\
    --in1 ${prefix}.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log \\
| gzip -c > ${prefix}.fastp.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 36 of fastp/main.nf 
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"""
[ ! -f  ${prefix}.fastq.gz ] && ln -sf $reads ${prefix}.fastq.gz

fastp \\
    --in1 ${prefix}.fastq.gz \\
    --out1  ${prefix}.fastp.fastq.gz \\
    --thread $task.cpus \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 57 of fastp/main.nf 
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"""
[ ! -f  ${prefix}_1.fastq.gz ] && ln -sf ${reads[0]} ${prefix}_1.fastq.gz
[ ! -f  ${prefix}_2.fastq.gz ] && ln -sf ${reads[1]} ${prefix}_2.fastq.gz
fastp \\
    --in1 ${prefix}_1.fastq.gz \\
    --in2 ${prefix}_2.fastq.gz \\
    --out1 ${prefix}_1.fastp.fastq.gz \\
    --out2 ${prefix}_2.fastp.fastq.gz \\
    --json ${prefix}.fastp.json \\
    --html ${prefix}.fastp.html \\
    $adapter_list \\
    $fail_fastq \\
    $merge_fastq \\
    --thread $task.cpus \\
    --detect_adapter_for_pe \\
    $args \\
    2> ${prefix}.fastp.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastp: \$(fastp --version 2>&1 | sed -e "s/fastp //g")
END_VERSIONS
"""
NextFlow fastp From line 78 of fastp/main.nf 
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"""
printf "%s %s\\n" $rename_to | while read old_name new_name; do
    [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
done
fastqc $args --threads $task.cpus $renamed_files

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
NextFlow FastQC From line 28 of fastqc/main.nf 
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"""
touch ${prefix}.html
touch ${prefix}.zip

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
NextFlow FastQC From line 42 of fastqc/main.nf 
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"""
gunzip \\
    -f \\
    $args \\
    $archive

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 23 of gunzip/main.nf 
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"""
touch $gunzip
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gunzip: \$(echo \$(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 37 of gunzip/main.nf 
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"""
samtools \\
    mpileup \\
    --reference $fasta \\
    $args2 \\
    $bam \\
    $mpileup \\
    | ivar \\
        consensus \\
        $args \\
        -p $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow SAMtools Consensus iVar From line 29 of consensus/main.nf 
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"""
ivar trim \\
    $args \\
    -i $bam \\
    -b $bed \\
    -p $prefix \\
    > ${prefix}.ivar.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow iVar From line 25 of trim/main.nf 
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"""
samtools \\
    mpileup \\
    $args2 \\
    --reference $fasta \\
    $bam \\
    $mpileup \\
    | ivar \\
        variants \\
        $args \\
        $features \\
        -r $fasta \\
        -p $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
"""
NextFlow SAMtools iVar From line 31 of variants/main.nf 
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"""
kraken2 \\
    --db $db \\
    --threads $task.cpus \\
    --report ${prefix}.kraken2.report.txt \\
    --gzip-compressed \\
    $unclassified_option \\
    $classified_option \\
    $readclassification_option \\
    $paired \\
    $args \\
    $reads

$compress_reads_command

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
    pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
NextFlow kraken2 From line 37 of kraken2/main.nf 
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"""
echo "${read_list}" | sed 's/,/\\n/g' > input_files.txt
minia \\
    $args \\
    -nb-cores $task.cpus \\
    -in input_files.txt \\
    -out $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
END_VERSIONS
"""
NextFlow Minia From line 26 of minia/main.nf 
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"""
mosdepth \\
    --threads $task.cpus \\
    $interval \\
    $reference \\
    $args \\
    $prefix \\
    $bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
END_VERSIONS
"""
NextFlow mosdepth From line 45 of mosdepth/main.nf 
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"""
touch ${prefix}.global.dist.txt
touch ${prefix}.region.dist.txt
touch ${prefix}.summary.txt
touch ${prefix}.per-base.d4
touch ${prefix}.per-base.bed.gz
touch ${prefix}.per-base.bed.gz.csi
touch ${prefix}.regions.bed.gz
touch ${prefix}.regions.bed.gz.csi
touch ${prefix}.quantized.bed.gz
touch ${prefix}.quantized.bed.gz.csi
touch ${prefix}.thresholds.bed.gz
touch ${prefix}.thresholds.bed.gz.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 62 of mosdepth/main.nf 
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"""
NanoPlot \\
    $args \\
    -t $task.cpus \\
    $input_file
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    nanoplot: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
END_VERSIONS
"""
NextFlow NanoPlot From line 27 of nanoplot/main.nf 
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"""
nextclade \\
    dataset \\
    get \\
    $args \\
    --name $dataset \\
    $fasta \\
    $version \\
    --output-dir $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//')
END_VERSIONS
"""
NextFlow nextclade From line 27 of datasetget/main.nf 
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"""
nextclade \\
    run \\
    $args \\
    --jobs $task.cpus \\
    --input-dataset $dataset \\
    --output-all ./ \\
    --output-basename ${prefix} \\
    $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//')
END_VERSIONS
"""
NextFlow nextclade From line 32 of run/main.nf 
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"""
pangolin \\
    $fasta\\
    --outfile ${prefix}.pangolin.csv \\
    --threads $task.cpus \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    pangolin: \$(pangolin --version | sed "s/pangolin //g")
END_VERSIONS
"""
NextFlow Pangolin From line 23 of pangolin/main.nf 
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"""
picard \\
    -Xmx${avail_mem}M \\
    CollectMultipleMetrics \\
    $args \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.CollectMultipleMetrics \\
    $reference

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard CollectMultipleMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 33 of collectmultiplemetrics/main.nf 
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"""
touch ${prefix}.CollectMultipleMetrics.alignment_summary_metrics
touch ${prefix}.CollectMultipleMetrics.insert_size_metrics
touch ${prefix}.CollectMultipleMetrics.quality_distribution.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle_metrics
touch ${prefix}.CollectMultipleMetrics.read_length_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.base_distribution_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.quality_by_cycle.pdf
touch ${prefix}.CollectMultipleMetrics.insert_size_histogram.pdf
touch ${prefix}.CollectMultipleMetrics.quality_distribution_metrics

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard CollectMultipleMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 50 of collectmultiplemetrics/main.nf 
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"""
picard \\
    -Xmx${avail_mem}M \\
    MarkDuplicates \\
    $args \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.bam \\
    --REFERENCE_SEQUENCE $fasta \\
    --METRICS_FILE ${prefix}.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 33 of markduplicates/main.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
touch ${prefix}.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 51 of markduplicates/main.nf 
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"""
plasmidID \\
    -d $fasta \\
    -s $prefix \\
    -c $scaffold \\
    $args \\
    -o .

mv NO_GROUP/$prefix ./$prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    plasmidid: \$(echo \$(plasmidID --version 2>&1))
END_VERSIONS
"""
NextFlow PlasmidID From line 31 of plasmidid/main.nf 
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"""
pycoQC \\
    $args \\
    -f $summary \\
    -o ${prefix}.html \\
    -j ${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    pycoqc: \$(pycoQC --version 2>&1 | sed 's/^.*pycoQC v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow pycoQC From line 24 of pycoqc/main.nf 
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"""
quast.py \\
    --output-dir $prefix \\
    $reference \\
    $features \\
    --threads $task.cpus \\
    $args \\
    ${consensus.join(' ')}

ln -s ${prefix}/report.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    quast: \$(quast.py --version 2>&1 | sed 's/^.*QUAST v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow QUAST From line 29 of quast/main.nf 
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"""
samtools \\
    flagstat \\
    --threads ${task.cpus} \\
    $bam \\
    > ${prefix}.flagstat

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 23 of flagstat/main.nf 
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"""
samtools \\
    idxstats \\
    --threads ${task.cpus-1} \\
    $bam \\
    > ${prefix}.idxstats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of idxstats/main.nf 
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"""
samtools \\
    index \\
    -@ ${task.cpus-1} \\
    $args \\
    $input

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 24 of index/main.nf 
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"""
touch ${input}.bai
touch ${input}.crai
touch ${input}.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 38 of index/main.nf 
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"""
samtools sort $args -@ $task.cpus -o ${prefix}.bam -T $prefix $bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 25 of sort/main.nf 
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"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 35 of sort/main.nf 
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"""
samtools \\
    stats \\
    --threads ${task.cpus} \\
    ${reference} \\
    ${input} \\
    > ${prefix}.stats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 25 of stats/main.nf 
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"""
touch ${prefix}.stats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 41 of stats/main.nf 
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"""
samtools \\
    view \\
    --threads ${task.cpus-1} \\
    ${reference} \\
    ${readnames} \\
    $args \\
    -o ${prefix}.${file_type} \\
    $input \\
    $args2

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 38 of view/main.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.cram

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 57 of view/main.nf 
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"""
spades.py \\
    $args \\
    --threads $task.cpus \\
    --memory $maxmem \\
    $custom_hmms \\
    $reads \\
    -o ./
mv spades.log ${prefix}.spades.log

if [ -f scaffolds.fasta ]; then
    mv scaffolds.fasta ${prefix}.scaffolds.fa
    gzip -n ${prefix}.scaffolds.fa
fi
if [ -f contigs.fasta ]; then
    mv contigs.fasta ${prefix}.contigs.fa
    gzip -n ${prefix}.contigs.fa
fi
if [ -f transcripts.fasta ]; then
    mv transcripts.fasta ${prefix}.transcripts.fa
    gzip -n ${prefix}.transcripts.fa
fi
if [ -f assembly_graph_with_scaffolds.gfa ]; then
    mv assembly_graph_with_scaffolds.gfa ${prefix}.assembly.gfa
    gzip -n ${prefix}.assembly.gfa
fi

if [ -f gene_clusters.fasta ]; then
    mv gene_clusters.fasta ${prefix}.gene_clusters.fa
    gzip -n ${prefix}.gene_clusters.fa
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow SPAdes From line 36 of spades/main.nf 
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"""
bgzip $command -c $args -@${task.cpus} $input > ${output}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 32 of bgzip/main.nf 
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"""
touch ${output}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 46 of bgzip/main.nf 
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"""
tabix $args $tab

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow tabix From line 23 of tabix/main.nf 
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"""
touch ${tab}.tbi
cat <<-END_VERSIONS > versions.yml

"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 34 of tabix/main.nf 
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"""
unicycler \\
    --threads $task.cpus \\
    $args \\
    $short_reads \\
    $long_reads \\
    --out ./

mv assembly.fasta ${prefix}.scaffolds.fa
gzip -n ${prefix}.scaffolds.fa
mv assembly.gfa ${prefix}.assembly.gfa
gzip -n ${prefix}.assembly.gfa
mv unicycler.log ${prefix}.unicycler.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    unicycler: \$(echo \$(unicycler --version 2>&1) | sed 's/^.*Unicycler v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow Unicycler From line 27 of unicycler/main.nf 
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"""
mkdir $prefix

## Ensures --strip-components only applied when top level of tar contents is a directory
## If just files or multiple directories, place all in prefix
if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then
    tar \\
        -C $prefix --strip-components 1 \\
        -xavf \\
        $args \\
        $archive \\
        $args2
else
    tar \\
        -C $prefix \\
        -xavf \\
        $args \\
        $archive \\
        $args2
fi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 25 of untar/main.nf 
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"""
mkdir $prefix
touch ${prefix}/file.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    untar: \$(echo \$(tar --version 2>&1) | sed 's/^.*(GNU tar) //; s/ Copyright.*\$//')
END_VERSIONS
"""
NextFlow From line 54 of untar/main.nf 
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"""
vcfuniq \\
    $vcf \\
    | bgzip -c $args > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    vcflib: $VERSION
END_VERSIONS
"""
NextFlow Vcflib From line 25 of vcfuniq/main.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/nf-core/viralrecon/blob/master/main.nf
Name: nf-core-viralrecon
Version: Version 1
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Copyright: Public Domain
License: MIT License
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