Call and score variants from WGS/WES of rare disease patients.

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Introduction

nf-core/raredisease is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by MIP .

The pipeline is built using Nextflow , a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from nf-core/modules in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!

On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the nf-core website .

Pipeline summary

1. Metrics:

2. Alignment:

3. Variant calling - SNV:

4. Variant calling - SV:

5. Annotation - SNV:

6. Annotation - SV:

7. Mitochondrial analysis:

8. Variant calling - repeat expansions:

9. Rank variants - SV and SNV:

Note that it is possible to include/exclude certain tools or steps.

Usage

Note If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

First, prepare a samplesheet with your input data that looks as follows:

samplesheet.csv : 

sample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id
hugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Second, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found here .

Now, you can run the pipeline using: 

nextflow run nf-core/raredisease \
 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> \
 --input samplesheet.csv \
 --outdir <OUTDIR>

Warning: Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters ; see docs .

For more details and further functionality, please refer to the usage documentation and the parameter documentation .

Pipeline output

For more details about the output files and reports, please refer to the output documentation .

Credits

nf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from Ramprasad Neethiraj , Anders Jemt , Lucia Pena Perez , and Mei Wu at Clinical Genomics Stockholm.

Additional contributors were Sima Rahimi , Gwenna Breton and Emma Västerviga (Clinical Genomics Gothenburg); Halfdan Rydbeck and Lauri Mesilaakso (Clinical Genomics Linköping); Subazini Thankaswamy Kosalai (Clinical Genomics Örebro); Annick Renevey and Peter Pruisscher (Clinical Genomics Stockholm); Ryan Kennedy (Clinical Genomics Lund); Anders Sune Pedersen (Danish National Genome Center) and Lucas Taniguti .

We thank the nf-core community for their extensive assistance in the development of this pipeline.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines .

For further information or help, don't hesitate to get in touch on the Slack #raredisease channel (you can join with this invite ).

Citations

If you use nf-core/raredisease for your analysis, please cite it using the following doi: 10.5281/zenodo.7995798

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x .

You can read more about MIP's use in healthcare in,

Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5

Code Snippets

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"""
add_most_severe_consequence.py --file_in ${vcf} --file_out ${prefix}.vcf --variant_csq ${variant_consequences}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    add_most_severe_consequence: v1.0
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 24 of local/add_most_severe_consequence.nf 
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"""
touch ${prefix}_csq.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    add_most_severe_consequence: v1.0
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 36 of local/add_most_severe_consequence.nf 
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"""
add_most_severe_pli.py --file_in ${vcf} --file_out ${prefix}.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    add_most_severe_pli: v1.0
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 23 of local/add_most_severe_pli.nf 
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"""
touch ${prefix}_pli.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    add_most_severe_pli: v1.0
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 35 of local/add_most_severe_pli.nf 
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"""
awk 'BEGIN {SEP="\t"}; {print \$1 SEP "0" SEP \$2}' ${fasta_fai} > ${fasta_fai.baseName}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
END_VERSIONS
"""
NextFlow From line 21 of local/create_bed_from_fai.nf 
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"""
touch chr.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
END_VERSIONS
"""
NextFlow From line 31 of local/create_bed_from_fai.nf 
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"""
vep \\
    -i $vcf \\
    -o ${prefix}.${file_extension}${compress_out} \\
    $args \\
    $reference \\
    --assembly $genome \\
    --species $species \\
    --cache \\
    --cache_version $cache_version \\
    --dir_cache $dir_cache \\
    --fork $task.cpus \\
    ${stats_file}


cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
NextFlow Variant Effect Predictor (VEP) From line 43 of ensemblvep/main.nf 
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"""
touch ${prefix}.vcf
touch ${prefix}.tab
touch ${prefix}.json
touch ${prefix}.vcf.gz
touch ${prefix}.tab.gz
touch ${prefix}.json.gz
touch ${prefix}.summary.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 66 of ensemblvep/main.nf 
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"""
filter_vep \\
    --format vcf \\
    --input_file $vcf \\
    --output_file ${prefix}.ann_filter.vcf.gz \\
    --only_matched \\
    --filter \"HGNC_ID in ${select_feature_file}\"

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 25 of local/filter_vep.nf 
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"""
touch ${prefix}.ann_filter.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 41 of local/filter_vep.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" CollectReadCounts \\
    -I $bam \\
    --read-index $bai \\
    -R $fasta \\
    -L $interval_list \\
    -O ${prefix}.hdf5 \\
    $args \\
    --tmp-dir .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 30 of collectreadcounts/main.nf 
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"""
touch ${prefix}.hdf5

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 48 of collectreadcounts/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" DenoiseReadCounts \\
    -I $read_counts \\
    --count-panel-of-normals $panel_of_normals \\
    --standardized-copy-ratios ${prefix}.standardizedCR.tsv \\
    --denoised-copy-ratios ${prefix}.denoisedCR.tsv \\
    $args \\
    --tmp-dir .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 28 of denoisereadcounts/main.nf 
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"""
touch ${prefix}.standardizedCR.tsv
touch ${prefix}.denoisedCR.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 45 of denoisereadcounts/main.nf 
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"""
generate_gens_data.pl \\
    $read_counts \\
    $vcf \\
    $prefix \\
    $gnomad_positions

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    generate_gens_data.pl: \$(echo \$(generate_gens_data.pl --version 2>&1))
END_VERSIONS
"""
NextFlow From line 19 of gens/main.nf 
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"""
touch ${prefix}.baf.bed.gz
touch ${prefix}.baf.bed.gz.tbi
touch ${prefix}.cov.bed.gz
touch ${prefix}.cov.bed.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    generate_gens_data.pl: \$(echo \$(generate_gens_data.pl --version 2>&1))
END_VERSIONS
"""
NextFlow From line 34 of gens/main.nf 
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"""
cut -f 1,2 $fai > ${fai}.sizes

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cut: \$(echo \$(cut --help 2>&1 | head -n 1 | cut -f1,2 -d' '))
END_VERSIONS
"""
NextFlow From line 21 of local/get_chrom_sizes.nf 
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"""
samtools stats --threads ${task.cpus} $args ${reference} ${input} | \\
grep -E ^IS | \\
awk 'BEGIN {sum=0} (\$2>=1200 && \$2<=15000) {sum=sum+\$3} (\$2<1200 || \$2>15000) {sum_norm=sum_norm+\$3} END \\
{print "intermediate discordant ", sum, "normal ", sum_norm, "ratio ppk", sum*1000/(sum_norm+sum)}' 1> ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 26 of local/mt_deletion_script.nf 
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"""
touch ${prefix}_mt_del.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 40 of local/mt_deletion_script.nf 
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"""
check_samplesheet.py \\
    $samplesheet \\
    samplesheet.valid.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    python: \$(python --version | sed 's/Python //g')
END_VERSIONS
"""
NextFlow From line 21 of local/samplesheet_check.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon driver  \\
    -t ${task.cpus} \\
    -r $fasta \\
    $args \\
    $input \\
    --algo QualCal \\
    $dbsnp \\
    ${prefix}.table

sentieon driver \\
    -t ${task.cpus} \\
    -r $fasta \\
    $args2 \\
    $input \\
    -q ${prefix}.table \\
    --algo QualCal \\
    $dbsnp \\
    ${prefix}.table_post \\
    --algo ReadWriter ${prefix}.bam

sentieon driver \\
    -t ${task.cpus} \\
    $args3 \\
    --algo QualCal \\
    --plot \\
    --before ${prefix}.table \\
    --after ${prefix}.table_post \\
    ${prefix}.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 33 of sentieon/bqsr.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
touch ${prefix}.table
touch ${prefix}.table_post
touch ${prefix}.csv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 76 of sentieon/bqsr.nf 
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"""
mkdir bwa

if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon bwa index \\
    $args \\
    -p $prefix \\
    $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
    bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA Sentieon DNASeq From line 21 of sentieon/bwamemindex.nf 
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"""
mkdir bwa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
    bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA From line 42 of sentieon/bwamemindex.nf 
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"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon bwa mem \\
    -t $task.cpus \\
    \$INDEX \\
    $reads \\
    $args \\
    | sentieon \\
        util \\
        sort \\
        -r $fasta \\
        -o ${prefix}.bam \\
        -t $task.cpus \\
        $args2 \\
        --sam2bam \\
        -i -

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
    bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA Sentieon DNASeq From line 26 of sentieon/bwamem.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bai

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
    bwa: \$(echo \$(sentieon bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA From line 58 of sentieon/bwamem.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon \\
    driver \\
    -t $task.cpus \\
    -r $fasta \\
    $input \\
    $args \\
    --algo GCBias --summary ${prefix}_gc_summary.txt ${prefix}_gc_metrics.txt \\
    --algo MeanQualityByCycle ${prefix}_mq_metrics.txt \\
    --algo QualDistribution ${prefix}_qd_metrics.txt \\
    --algo InsertSizeMetricAlgo ${prefix}_is_metrics.txt  \\
    --algo AlignmentStat ${prefix}_aln_metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 29 of sentieon/datametrics.nf 
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"""
touch ${prefix}_mq_metrics.txt
touch ${prefix}_qd_metrics.txt
touch ${prefix}_gc_summary.txt
touch ${prefix}_gc_metrics.txt
touch ${prefix}_aln_metrics.txt
touch ${prefix}_is_metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 55 of sentieon/datametrics.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon \\
    driver \\
    -t $task.cpus \\
    $input \\
    $args \\
    --algo Dedup \\
    --score_info $score \\
    --metrics ${prefix}_metrics.txt \\
    ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 26 of sentieon/dedup.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bam.bai
touch ${prefix}_metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 50 of sentieon/dedup.nf 
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"""
sentieon driver \\
    -t $task.cpus \\
    -r $fasta \\
    --algo DNAModelApply \\
    --model $ml_model \\
    -v $vcf \\
    ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 24 of sentieon/dnamodelapply.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" )
END_VERSIONS
"""
NextFlow From line 41 of sentieon/dnamodelapply.nf 
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"""
sentieon driver \\
    -t $task.cpus \\
    -r $fasta \\
    $args \\
    -i $bam \\
    --algo DNAscope \\
    $dbsnp \\
    $interval \\
    $args2 \\
    $model \\
    ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 32 of sentieon/dnascope.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g" )
END_VERSIONS
"""
NextFlow From line 53 of sentieon/dnascope.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon \\
    driver \\
    -t $task.cpus \\
    $input \\
    --algo LocusCollector \\
    --fun score_info $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 22 of sentieon/locuscollector.nf 
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"""
touch ${prefix}.txt.gz
touch ${prefix}.txt.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 43 of sentieon/locuscollector.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon \\
    driver \\
    -t $task.cpus \\
    $input \\
    --algo ReadWriter \\
    ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 24 of sentieon/readwriter.nf 
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"""
touch ${prefix}.bam
touch ${prefix}.bam.bai

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 45 of sentieon/readwriter.nf 
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"""
if [ \${SENTIEON_LICENSE_BASE64:-"unset"} != "unset" ]; then
    echo "Initializing SENTIEON_LICENSE env variable"
    source sentieon_init.sh SENTIEON_LICENSE_BASE64
fi

sentieon \\
    driver \\
    -t $task.cpus \\
    -r $fasta \\
    $input \\
    $interval \\
    $args \\
    --algo WgsMetricsAlgo ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow Sentieon DNASeq From line 26 of sentieon/wgsmetricsalgo.nf 
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"""
touch ${prefix}_wgs_metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS
"""
NextFlow From line 49 of sentieon/wgsmetricsalgo.nf 
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"""
bcftools \\
    annotate \\
    $args \\
    $annotations_file \\
    $header_file \\
    --output ${prefix}.${extension} \\
    --threads $task.cpus \\
    $input

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS
"""
NextFlow BCFtools From line 31 of annotate/main.nf 
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"""
touch ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS
"""
NextFlow BCFtools From line 55 of annotate/main.nf 
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"""
bcftools concat \\
    --output ${prefix}.vcf.gz \\
    $args \\
    --threads $task.cpus \\
    ${vcfs}

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 concat/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 concat/main.nf 
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"""
bcftools filter \\
    --output ${prefix}.${extension} \\
    --threads ${task.cpus} \\
    $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 32 of filter/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 56 of filter/main.nf 
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"""
bcftools merge \\
    $args \\
    $regions \\
    --threads $task.cpus \\
    --output ${prefix}.${extension} \\
    $vcfs

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 34 of merge/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 56 of merge/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 \\
    reheader \\
    $update_sequences \\
    $new_header \\
    $args \\
    --threads $task.cpus \\
    $vcf \\
    | bcftools view \\
    $args2 \\
    --output ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow BCFtools From line 33 of reheader/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 60 of reheader/main.nf 
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"""
bcftools \\
    roh \\
    $args \\
    $af_read \\
    $gen_map \\
    $reg_file \\
    $samp_file \\
    $targ_file \\
    -o ${prefix}.roh \\
    $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 33 of roh/main.nf 
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"""
touch ${prefix}.roh

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 53 of roh/main.nf 
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"""
bcftools view \\
    --output ${prefix}.vcf.gz \\
    ${regions_file} \\
    ${targets_file} \\
    ${samples_file} \\
    $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 29 of view/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 47 of view/main.nf 
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"""
mkdir bwa
bwa \\
    index \\
    $args \\
    -p bwa/${fasta.baseName} \\
    $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA From line 22 of index/main.nf 
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"""
mkdir bwa

touch bwa/genome.amb
touch bwa/genome.ann
touch bwa/genome.bwt
touch bwa/genome.pac
touch bwa/genome.sa

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
END_VERSIONS
"""
NextFlow BWA From line 37 of index/main.nf 
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"""
mkdir bwamem2
bwa-mem2 \\
    index \\
    $args \\
    $fasta -p bwamem2/${fasta}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS
"""
NextFlow Bwa-mem2 From line 22 of index/main.nf 
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"""
mkdir bwamem2
touch bwamem2/${fasta}.0123
touch bwamem2/${fasta}.ann
touch bwamem2/${fasta}.pac
touch bwamem2/${fasta}.amb
touch bwamem2/${fasta}.bwt.2bit.64

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
END_VERSIONS
"""
NextFlow Bwa-mem2 From line 36 of index/main.nf 
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"""
INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`

bwa-mem2 \\
    mem \\
    $args \\
    -t $task.cpus \\
    \$INDEX \\
    $reads \\
    | samtools $samtools_command $args2 -@ $task.cpus -o ${prefix}.bam -

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools Bwa-mem2 From line 27 of mem/main.nf 
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"""
touch ${prefix}.bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed 's/.* //')
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 47 of mem/main.nf 
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"""
cadd.sh \\
    -o ${prefix}.tsv.gz \\
    $args \\
    $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cadd: $VERSION
END_VERSIONS
"""
NextFlow From line 31 of cadd/main.nf 
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"""
touch ${prefix}.tsv.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    cadd: $VERSION
END_VERSIONS
"""
NextFlow From line 47 of cadd/main.nf 
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"""
$command1 \\
    $args \\
    ${file_list.join(' ')} \\
    $command2 \\
    > ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
NextFlow From line 38 of cat/main.nf 
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"""
touch $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
NextFlow From line 54 of cat/main.nf 
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"""
chromograph \\
    $args \\
    $autozyg_param \\
    $coverage_param \\
    $exome_param \\
    $fracsnp_param \\
    $ideogram_param \\
    $regions_param \\
    $sites_param \\
    --outd ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
END_VERSIONS
"""
NextFlow From line 51 of chromograph/main.nf 
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"""
mkdir ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    chromograph: \$(echo \$(chromograph --version 2>&1) | sed 's/chromograph //' )
END_VERSIONS
"""
NextFlow From line 87 of chromograph/main.nf 
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"""
/opt/deepvariant/bin/run_deepvariant \\
    --ref=${fasta} \\
    --reads=${input} \\
    --output_vcf=${prefix}.vcf.gz \\
    --output_gvcf=${prefix}.g.vcf.gz \\
    ${args} \\
    ${regions} \\
    --intermediate_results_dir=. \\
    --num_shards=${task.cpus}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS
"""
NextFlow From line 33 of deepvariant/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
touch ${prefix}.g.vcf.gz
touch ${prefix}.g.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    deepvariant: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' )
END_VERSIONS
"""
NextFlow From line 52 of deepvariant/main.nf 
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"""
echo "$bam\t${prefix}" > infile.txt
eKLIPse.py \\
    -in infile.txt \\
    -ref $ref_gb
mv eKLIPse_*/eKLIPse_deletions.csv eKLIPse_deletions.csv
mv eKLIPse_*/eKLIPse_genes.csv eKLIPse_genes.csv
mv eKLIPse_*/eKLIPse_${prefix}.png eKLIPse_${prefix}.png

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    eklipse: $VERSION
END_VERSIONS
"""
NextFlow From line 30 of eklipse/main.nf 
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"""
touch eKLIPse_deletions.csv
touch eKLIPse_genes.csv
touch eKLIPse_${prefix}.png

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    eklipse: $VERSION
END_VERSIONS
"""
NextFlow From line 48 of eklipse/main.nf 
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"""
ExpansionHunter \\
    ${args} \\
    --reads ${bam} \\
    --output-prefix ${prefix} \\
    --reference ${fasta} \\
    --variant-catalog ${variant_catalog}

bgzip --threads ${task.cpus} ${args2} ${prefix}.vcf
bgzip --threads ${task.cpus} ${args2} ${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
    bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//')
END_VERSIONS
"""
NextFlow ExpansionHunter Denovo From line 29 of expansionhunter/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.json.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    expansionhunter: \$( echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter v//')
    bgzip: \$(echo \$(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//')
END_VERSIONS
"""
NextFlow From line 49 of expansionhunter/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
"${task.process}":
    fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
END_VERSIONS
"""
NextFlow FastQC From line 46 of fastqc/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" BedToIntervalList \\
    --INPUT $bed \\
    --OUTPUT ${prefix}.interval_list \\
    --SEQUENCE_DICTIONARY $dict \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 31 of bedtointervallist/main.nf 
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"""
touch ${prefix}.interval_list

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 47 of bedtointervallist/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" CollectReadCounts \\
    --input $input \\
    --intervals $intervals \\
    --output ${prefix}.$extension \\
    $reference \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 39 of collectreadcounts/main.nf 
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"""
touch ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 60 of collectreadcounts/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" CreateSequenceDictionary \\
    --REFERENCE $fasta \\
    --URI $fasta \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 29 of createsequencedictionary/main.nf 
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"""
touch ${fasta.baseName}.dict

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 43 of createsequencedictionary/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" DetermineGermlineContigPloidy \\
    ${input_list} \\
    --output ./ \\
    --output-prefix ${prefix} \\
    ${intervals} \\
    ${exclude} \\
    ${contig_ploidy} \\
    ${model} \\
    --tmp-dir . \\
    ${args}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 42 of determinegermlinecontigploidy/main.nf 
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"""
touch ${prefix}-calls
touch ${prefix}-model

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 62 of determinegermlinecontigploidy/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" FilterMutectCalls \\
    --variant $vcf \\
    --output ${prefix}.vcf.gz \\
    --reference $fasta \\
    $orientationbias_command \\
    $segmentation_command \\
    $estimate_command \\
    $table_command \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 40 of filtermutectcalls/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
touch ${prefix}.vcf.gz.filteringStats.tsv

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 60 of filtermutectcalls/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}g" GermlineCNVCaller \\
    $input_list \\
    $ploidy_command \\
    $output_command \\
    --output-prefix $prefix \\
    $args \\
    $intervals_command \\
    $model_command

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 39 of germlinecnvcaller/main.nf 
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"""
mkdir -p ${prefix}-cnv-calls/${prefix}-calls
mkdir -p ${prefix}-cnv-model/${prefix}-model

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 57 of germlinecnvcaller/main.nf 
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"""

mkdir ${prefix}_split

gatk --java-options "-Xmx${avail_mem}M" IntervalListTools \\
    --INPUT $intervals \\
    --OUTPUT ${prefix}_split \\
    --TMP_DIR . \\
    $args

python3 <<CODE
import glob, os
# The following python code snippet rename the output files into different name to avoid overwriting or name conflict
intervals = sorted(glob.glob("*_split/*/*.interval_list"))
for i, interval in enumerate(intervals):
    (directory, filename) = os.path.split(interval)
    newName = os.path.join(directory, str(i + 1) + filename)
    os.rename(interval, newName)
CODE

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 30 of intervallisttools/main.nf 
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"""
mkdir -p ${prefix}_split/temp_0001_of_6
mkdir -p ${prefix}_split/temp_0002_of_6
mkdir -p ${prefix}_split/temp_0003_of_6
mkdir -p ${prefix}_split/temp_0004_of_6
touch ${prefix}_split/temp_0001_of_6/1scattered.interval_list
touch ${prefix}_split/temp_0002_of_6/2scattered.interval_list
touch ${prefix}_split/temp_0003_of_6/3scattered.interval_list
touch ${prefix}_split/temp_0004_of_6/4scattered.interval_list

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 58 of intervallisttools/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" MergeBamAlignment \\
    --UNMAPPED_BAM $unmapped \\
    --ALIGNED_BAM $aligned \\
    --OUTPUT ${prefix}.bam \\
    --REFERENCE_SEQUENCE $fasta \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 32 of mergebamalignment/main.nf 
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"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 49 of mergebamalignment/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" MergeVcfs \\
    $input_list \\
    --OUTPUT ${prefix}.vcf.gz \\
    $reference_command \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 34 of mergevcfs/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 50 of mergevcfs/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" Mutect2 \\
    $inputs \\
    --output ${prefix}.vcf.gz \\
    --reference $fasta \\
    $pon_command \\
    $gr_command \\
    $interval_command \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 44 of mutect2/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi
touch ${prefix}.vcf.gz.stats
touch ${prefix}.f1r2.tar.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 63 of mutect2/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}g" PostprocessGermlineCNVCalls \\
    $calls_command \\
    $model_command \\
    $ploidy_command \\
    --output-genotyped-intervals ${prefix}_genotyped_intervals.vcf.gz \\
    --output-genotyped-segments ${prefix}_genotyped_segments.vcf.gz \\
    --output-denoised-copy-ratios ${prefix}_denoised.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 38 of postprocessgermlinecnvcalls/main.nf 
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"""
touch ${prefix}_genotyped_intervals.vcf.gz
touch ${prefix}_genotyped_segments.vcf.gz
touch ${prefix}_denoised.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 55 of postprocessgermlinecnvcalls/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" PreprocessIntervals \\
    $include_command \\
    $exclude_command \\
    --reference $fasta \\
    --output ${prefix}.interval_list \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 37 of preprocessintervals/main.nf 
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"""
touch ${prefix}.interval_list

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 53 of preprocessintervals/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" PrintReads \\
    $args \\
    --reference $fasta \\
    --input $input \\
    --read-index $index \\
    --output ${prefix}.${input.getExtension()}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 38 of printreads/main.nf 
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"""
touch ${prefix}.${input.getExtension()}
touch ${prefix}.${input.getExtension()}
touch ${prefix}.${input.getExtension()}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 54 of printreads/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" RevertSam \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.reverted.bam \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 30 of revertsam/main.nf 
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"""
touch ${prefix}.reverted.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 45 of revertsam/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" SamToFastq \\
    --INPUT $bam \\
    $output \\
    --TMP_DIR . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 31 of samtofastq/main.nf 
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"""
touch ${prefix}.fastq.gz
touch ${prefix}_1.fastq.gz
touch ${prefix}_2.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 46 of samtofastq/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" SelectVariants \\
    --variant $vcf \\
    --output ${prefix}.selectvariants.vcf.gz \\
    $interval \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 32 of selectvariants/main.nf 
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"""
touch ${prefix}.selectvariants.vcf.gz
touch ${prefix}.selectvariants.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 48 of selectvariants/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" ShiftFasta \\
    --reference $fasta \\
    --output ${prefix}_shift.fasta \\
    --shift-back-output ${prefix}_shift.back_chain \\
    $args \\
    $seq_dict \\
    --tmp-dir .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 38 of shiftfasta/main.nf 
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"""
touch test.intervals
touch test_shift.back_chain
touch test_shift.dict
touch test.shifted.intervals
touch test_shift.fasta
touch test_shift.fasta.fai

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 54 of shiftfasta/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" SplitIntervals \\
    --output ${prefix} \\
    --intervals $intervals \\
    $reference \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 34 of splitintervals/main.nf 
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"""
mkdir ${prefix}
touch ${prefix}/0000-scattered.interval_list
touch ${prefix}/0001-scattered.interval_list

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 50 of splitintervals/main.nf 
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"""
gatk --java-options "-Xmx${avail_mem}M" VariantFiltration \\
    --variant $vcf \\
    --output ${prefix}.vcf.gz \\
    --reference $fasta \\
    --tmp-dir . \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow gatk From line 34 of variantfiltration/main.nf 
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"""
touch ${prefix}.vcf.gz
touch ${prefix}.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 49 of variantfiltration/main.nf 
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"""
genmod \\
    annotate \\
    $args \\
    --outfile ${prefix}_annotate.vcf \\
    $input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow GENMOD From line 23 of annotate/main.nf 
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"""
touch ${prefix}_annotate.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow From line 38 of annotate/main.nf 
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"""
genmod \\
    compound \\
    $args \\
    --processes ${task.cpus} \\
    --outfile ${prefix}_compound.vcf \\
    $input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow GENMOD From line 23 of compound/main.nf 
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"""
touch ${prefix}_compound.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow From line 39 of compound/main.nf 
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"""
genmod \\
    models \\
    $args \\
    $pen_file \\
    $family_file \\
    --processes ${task.cpus} \\
    --outfile ${prefix}_models.vcf \\
    $input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow GENMOD From line 27 of models/main.nf 
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"""
touch ${prefix}_models.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow From line 45 of models/main.nf 
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"""
genmod \\
    score \\
    $args \\
    $family_file \\
    $config_file \\
    --outfile ${prefix}_score.vcf \\
    $input_vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow GENMOD From line 27 of score/main.nf 
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"""
touch ${prefix}_score.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
END_VERSIONS
"""
NextFlow From line 44 of score/main.nf 
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"""
glnexus_cli \\
    --threads $task.cpus \\
    --mem-gbytes $avail_mem \\
    $args \\
    ${input.join(' ')} \\
    > ${prefix}.bcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow GLnexus From line 32 of glnexus/main.nf 
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"""
touch ${prefix}.bcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    glnexus: \$( echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release v//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 48 of glnexus/main.nf 
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"""
haplocheck --raw --out $prefix $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' )
END_VERSIONS
"""
NextFlow haplocheck From line 24 of haplocheck/main.nf 
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"""
touch ${prefix}.raw.txt
touch ${prefix}.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    haplocheck: \$(echo \$(haplocheck --version 2>&1) | sed 's/.*\\([0-9].[0-9].[0-9]\\).*/\\1/' )
END_VERSIONS
"""
NextFlow From line 35 of haplocheck/main.nf 
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"""
haplogrep \\
    classify \\
    $args \\
    --in $inputfile \\
    --out ${prefix}.txt \\
    --format $format

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    haplogrep2: \$(echo \$(haplogrep --version 2>&1) | (sed 's/htt.*//') | (sed 's/.*v//'))
END_VERSIONS
"""
NextFlow HaploGrep From line 24 of classify/main.nf 
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"""
touch ${prefix}.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    haplogrep2: \$(echo \$(haplogrep --version 2>&1) | (sed 's/htt.*//') | (sed 's/.*v//'))
END_VERSIONS
"""
NextFlow From line 40 of classify/main.nf 
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"""
hmtnote \\
    annotate \\
    $vcf \\
    ${prefix}_annotated.vcf \\
    $args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
END_VERSIONS
"""
NextFlow hmtnote From line 24 of annotate/main.nf 
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"""
touch ${prefix}_annotated.vcf
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
END_VERSIONS
"""
NextFlow From line 38 of annotate/main.nf 
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"""
configManta.py \
    ${input_files} \
    --reference $fasta \
    --runDir manta \
    $options_manta \
    $args

python manta/runWorkflow.py -m local -j $task.cpus

mv manta/results/variants/candidateSmallIndels.vcf.gz \
    ${prefix}.candidate_small_indels.vcf.gz
mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi \
    ${prefix}.candidate_small_indels.vcf.gz.tbi
mv manta/results/variants/candidateSV.vcf.gz \
    ${prefix}.candidate_sv.vcf.gz
mv manta/results/variants/candidateSV.vcf.gz.tbi \
    ${prefix}.candidate_sv.vcf.gz.tbi
mv manta/results/variants/diploidSV.vcf.gz \
    ${prefix}.diploid_sv.vcf.gz
mv manta/results/variants/diploidSV.vcf.gz.tbi \
    ${prefix}.diploid_sv.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    manta: \$( configManta.py --version )
END_VERSIONS
"""
NextFlow manta From line 34 of germline/main.nf 
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"""
touch ${prefix}.candidate_small_indels.vcf.gz
touch ${prefix}.candidate_small_indels.vcf.gz.tbi
touch ${prefix}.candidate_sv.vcf.gz
touch ${prefix}.candidate_sv.vcf.gz.tbi
touch ${prefix}.diploid_sv.vcf.gz
touch ${prefix}.diploid_sv.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    manta: \$( configManta.py --version )
END_VERSIONS
"""
NextFlow From line 65 of germline/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 44 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 61 of mosdepth/main.nf 
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"""
multiqc \\
    --force \\
    $args \\
    $config \\
    $extra_config \\
    .

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
NextFlow MultiQC From line 28 of multiqc/main.nf 
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"""
touch multiqc_data
touch multiqc_plots
touch multiqc_report.html

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS
"""
NextFlow MultiQC From line 43 of multiqc/main.nf 
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"""
peddy \\
    $args \\
    --prefix $prefix \\
    --plot \\
    -p $task.cpus \\
    $vcf \\
    $ped

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    peddy: \$( peddy --version 2>&1 | sed 's/peddy, version //' )
END_VERSIONS
"""
NextFlow peddy From line 27 of peddy/main.nf 
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"""
touch ${prefix}.ped_check.csv
touch ${prefix}.vs.html
touch ${prefix}.het_check.csv
touch ${prefix}.sex_check.csv
touch ${prefix}.peddy.ped
touch ${prefix}.html

touch versions.yml
"""
NextFlow From line 44 of peddy/main.nf 
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"""
picard \\
    -Xmx${avail_mem}M \\
    AddOrReplaceReadGroups \\
    $args \\
    --INPUT ${bam} \\
    --OUTPUT ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 30 of addorreplacereadgroups/main.nf 
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"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 46 of addorreplacereadgroups/main.nf 
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"""

$bait_intervallist_cmd
$target_intervallist_cmd

picard \\
    -Xmx${avail_mem}M \\
    CollectHsMetrics \\
    $args \\
    $reference \\
    --BAIT_INTERVALS $bait_interval_list \\
    --TARGET_INTERVALS $target_interval_list \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.CollectHsMetrics.coverage_metrics


cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 50 of collecthsmetrics/main.nf 
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"""
touch ${prefix}.CollectHsMetrics.coverage_metrics

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard CollectHsMetrics --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 74 of collecthsmetrics/main.nf 
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"""
picard \\
    -Xmx${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 \\
    CollectWgsMetrics \\
    $args \\
    --INPUT $bam \\
    --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
    --REFERENCE_SEQUENCE ${fasta} \\
    $interval


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

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard CollectWgsMetrics --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 52 of collectwgsmetrics/main.nf 
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"""
picard \\
    -Xmx${avail_mem}M \\
    LiftoverVcf \\
    $args \\
    --INPUT $input_vcf \\
    --OUTPUT ${prefix}.lifted.vcf.gz \\
    --CHAIN $chain \\
    --REJECT ${prefix}.unlifted.vcf.gz \\
    --REFERENCE_SEQUENCE $fasta

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 33 of liftovervcf/main.nf 
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"""
touch ${prefix}.lifted.vcf.gz
touch ${prefix}.unlifted.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(echo \$(picard LiftoverVcf --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 52 of liftovervcf/main.nf 
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"""
picard \\
    -Xmx${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
"${task.process}":
    picard: \$(echo \$(picard MarkDuplicates --version 2>&1) | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 51 of markduplicates/main.nf 
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"""
picard \\
    RenameSampleInVcf \\
    -Xmx${avail_mem}M \\
    --INPUT $vcf \\
    --OUTPUT ${prefix}_renam.vcf.gz \\
    $extended_args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 32 of renamesampleinvcf/main.nf 
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"""
touch ${prefix}_renam.vcf.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard RenameSampleInVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 49 of renamesampleinvcf/main.nf 
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"""
picard \\
    SortVcf \\
    -Xmx${avail_mem}M \\
    --INPUT $vcf \\
    $args \\
    $seq_dict \\
    $reference \\
    --OUTPUT ${prefix}_sorted.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow Picard From line 34 of sortvcf/main.nf 
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"""
touch ${prefix}_sorted.vcf.gz
touch ${prefix}.bam.bai
touch ${prefix}.MarkDuplicates.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    picard: \$(picard SortVcf --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
END_VERSIONS
"""
NextFlow From line 52 of sortvcf/main.nf 
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"""
unset DISPLAY
mkdir -p tmp
export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp
qualimap \\
    --java-mem-size=$memory \\
    bamqc \\
    $args \\
    -bam $bam \\
    $regions \\
    -p $strandedness \\
    $collect_pairs \\
    -outdir $prefix \\
    -nt $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
NextFlow QualiMap From line 35 of bamqc/main.nf 
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"""
mkdir -p $prefix/css
mkdir $prefix/images_qualimapReport
mkdir $prefix/raw_data_qualimapReport
cd $prefix/css
touch agogo.css
touch basic.css
touch bgtop.png
touch comment-close.png
touch doctools.js
touch down-pressed.png
touch jquery.js
touch plus.png
touch qualimap_logo_small.png
touch searchtools.js
touch up.png
touch websupport.js
touch ajax-loader.gif
touch bgfooter.png
touch comment-bright.png
touch comment.png
touch down.png
touch file.png
touch minus.png
touch pygments.css
touch report.css
touch underscore.js
touch up-pressed.png
cd ../images_qualimapReport/
touch genome_coverage_0to50_histogram.png
touch genome_coverage_quotes.png
touch genome_insert_size_across_reference.png
touch genome_mapping_quality_histogram.png
touch genome_uniq_read_starts_histogram.png
touch genome_coverage_across_reference.png
touch genome_gc_content_per_window.png
touch genome_insert_size_histogram.png
touch genome_reads_clipping_profile.png
touch genome_coverage_histogram.png
touch genome_homopolymer_indels.png
touch genome_mapping_quality_across_reference.png
touch genome_reads_content_per_read_position.png
cd ../raw_data_qualimapReport
touch coverage_across_reference.txt
touch genome_fraction_coverage.txt
touch insert_size_histogram.txt
touch mapped_reads_nucleotide_content.txt
touch coverage_histogram.txt
touch homopolymer_indels.txt
touch mapped_reads_clipping_profile.txt
touch mapping_quality_across_reference.txt
touch duplication_rate_histogram.txt
touch insert_size_across_reference.txt
touch mapped_reads_gc-content_distribution.txt
touch mapping_quality_histogram.txt
cd ../
touch genome_results.txt
touch qualimapReport.html
cd ../

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//')
END_VERSIONS
"""
NextFlow From line 58 of bamqc/main.nf 
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"""
rhocall \\
    annotate \\
    $args \\
    $az_bed \\
    -r $roh \\
    -o ${prefix}_rhocall.vcf \\
    $vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
END_VERSIONS
"""
NextFlow rhocall From line 26 of annotate/main.nf 
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"""
touch ${prefix}_rhocall.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
END_VERSIONS
"""
NextFlow From line 43 of annotate/main.nf 
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"""
samtools \\
    faidx \\
    $fasta \\
    $args

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 faidx/main.nf 
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"""
${fastacmd}
touch ${fasta}.fai

cat <<-END_VERSIONS > versions.yml

"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 40 of faidx/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 \\
    merge \\
    --threads ${task.cpus-1} \\
    $args \\
    ${reference} \\
    ${prefix}.${file_type} \\
    $input_files

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SAMtools From line 30 of merge/main.nf 
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"""
touch ${prefix}.${file_type}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 48 of merge/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 41 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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"""
echo $bam | tr ' ' '
' > manifest.txt
smn_caller.py \\
    $args \\
    --manifest manifest.txt \\
    --prefix $prefix \\
    --outDir "out" \\
    --threads $task.cpus

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    SMNCopyNumberCaller: $VERSION
END_VERSIONS
"""
NextFlow smncopynumbercaller From line 25 of smncopynumbercaller/main.nf 
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"""
mkdir out
touch out/${prefix}.tsv
touch out/${prefix}.json

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    SMNCopyNumberCaller: $VERSION
END_VERSIONS
"""
NextFlow From line 44 of smncopynumbercaller/main.nf 
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"""
stranger \\
    $args \\
    $vcf \\
    $options_variant_catalog | gzip --no-name > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    stranger: \$( stranger --version )
END_VERSIONS
"""
NextFlow Stranger From line 25 of stranger/main.nf 
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"""
touch ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    stranger: \$( stranger --version )
END_VERSIONS
"""
NextFlow Stranger From line 39 of stranger/main.nf 
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"""
svdb \\
    --merge \\
    $args \\
    $prio \\
    --vcf $input \\
    > ${prefix}_sv_merge.vcf
bgzip ${prefix}_sv_merge.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow SVDB From line 32 of merge/main.nf 
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"""
touch ${prefix}_sv_merge.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
    samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
NextFlow From line 50 of merge/main.nf 
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"""
svdb \\
    --query \\
    $in_occ \\
    $in_frq \\
    $out_occ \\
    $out_frq \\
    $args \\
    --db ${vcf_dbs.join(',')} \\
    --query_vcf $vcf \\
    --prefix ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS
"""
NextFlow SVDB From line 45 of query/main.nf 
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"""
touch ${prefix}_query.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
END_VERSIONS
"""
NextFlow From line 65 of query/main.nf 
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"""
bgzip  --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
tabix $args2 ${prefix}.${input.getExtension()}.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow tabix From line 25 of bgziptabix/main.nf 
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"""
touch ${prefix}.${input.getExtension()}.gz
touch ${prefix}.${input.getExtension()}.gz.tbi
touch ${prefix}.${input.getExtension()}.gz.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 37 of bgziptabix/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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"""
tiddit \\
    --cov \\
    -o $prefix \\
    $args \\
    --bam $input \\
    $reference

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
NextFlow TIDDIT From line 26 of cov/main.nf 
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"""
touch ${prefix}.wig
touch ${prefix}.tab

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 42 of cov/main.nf 
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"""
$bwa_command

tiddit \\
    --sv \\
    $args \\
    --bam $input \\
    --ref $fasta \\
    -o $prefix

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
NextFlow TIDDIT From line 28 of sv/main.nf 
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"""
touch ${prefix}.vcf
touch ${prefix}.ploidies.tab

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    tiddit: \$(echo \$(tiddit 2>&1) | sed 's/^.*tiddit-//; s/ .*\$//')
END_VERSIONS
"""
NextFlow From line 46 of sv/main.nf 
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"""
wigToBigWig \\
    $args \\
    $wig \\
    $sizes \\
    ${prefix}.bw

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ucsc: $VERSION
END_VERSIONS
"""
NextFlow wigToBigWig From line 26 of wigtobigwig/main.nf 
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"""
touch ${prefix}.bw

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    ucsc: $VERSION
END_VERSIONS
"""
NextFlow From line 42 of wigtobigwig/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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"""
upd \\
    --vcf $vcf \\
    $args \\
    | sort -k 1,1 -k 2,2n >${prefix}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    upd: \$( upd --version 2>&1 | sed 's/upd, version //' )
END_VERSIONS
"""
NextFlow From line 24 of upd/main.nf 
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"""
touch ${prefix}.bed

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    upd: \$( upd --version 2>&1 | sed 's/upd, version //' )
END_VERSIONS
"""
NextFlow From line 38 of upd/main.nf 
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"""
vcfanno \\
    -p ${task.cpus} \\
    ${args} \\
    ${lua_cmd} \\
    ${toml} \\
    ${vcf} \\
    > ${prefix}.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
END_VERSIONS
"""
NextFlow vcfanno From line 27 of vcfanno/main.nf 
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"""
touch ${prefix}.vcf

cat <<-END_VERSIONS > versions.yml
"${task.process}":
    vcfanno: \$(echo \$(vcfanno 2>&1 | grep version | cut -f3 -d' ' ))
END_VERSIONS
"""
NextFlow From line 44 of vcfanno/main.nf
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://nf-co.re/raredisease
Name: raredisease
Version: 1.0.0
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Copyright: Public Domain
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