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Annotation.nf
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Annotation.nf
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#!/usr/bin/env nextflow
/*
* AUTHOR: CERC Genomic Medicine, Daniel Taliun, PhD <[email protected]>
* VERSION: 3.0
* YEAR: 2022
*/
process vcf_by_chrom {
label "VEP"
cache "lenient"
executor "local"
cpus 1
input:
tuple path(vcf), path(vcf_index)
output:
tuple stdout, path(vcf), path(vcf_index)
"""
tabix -l ${vcf} | tr "\n" ","
"""
}
process annotate_chunks {
label "VEP"
cache "lenient"
scratch true
errorStrategy { sleep(Math.pow(2, task.attempt) * 200 as long); return "retry" }
maxRetries 3
cpus 1
containerOptions "-B ${params.vep_cache}:/opt/vep/.vep"
input:
tuple val(chrom), path(vcf), path(vcf_index), val(start), val(stop)
output:
tuple(val(chrom), val("${vcf.getSimpleName()}"), path("${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.vcf.gz"), emit: annotations)
path "*.vep.log", emit: logs
publishDir "results/logs", pattern: "*.vep.log", mode: "copy"
script:
if (params.assembly == "GRCh38")
"""
export PERL5LIB=/opt/vep/.vep/Plugins/:\$PERL5LIB
loftee_args=human_ancestor_fa:/opt/vep/.vep/loftee_db_${params.assembly}/human_ancestor.fa.gz,gerp_bigwig:/opt/vep/.vep/loftee_db_${params.assembly}/gerp_conservation_scores.homo_sapiens.GRCh38.bw,conservation_file:/opt/vep/.vep/loftee_db_${params.assembly}/loftee.sql${params.loftee_flags}
bcftools view ${params.drop_genotypes} ${vcf} ${chrom}:${start}-${stop} | vep --cache --offline --assembly ${params.assembly} --format vcf --vcf --compress_output bgzip --force_overwrite --dir_cache /opt/vep/.vep/ --plugin LoF,loftee_path:/opt/vep/.vep/loftee_${params.assembly},\${loftee_args} --dir_plugins /opt/vep/.vep/loftee_${params.assembly} --plugin CADD,/opt/vep/.vep/CADD_${params.assembly}/whole_genome_SNVs.tsv.gz,/opt/vep/.vep/CADD_${params.assembly}/gnomad.genomes.r4.0.indel.tsv.gz --plugin CONTEXT ${params.vep_flags} --warning_file STDERR --output_file STDOUT > ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.vcf.gz 2> ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.log
sanity_check.py -a ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.vcf.gz
"""
else if (params.assembly == "GRCh37")
"""
export PERL5LIB=/opt/vep/.vep/Plugins/:\$PERL5LIB
loftee_args=human_ancestor_fa:/opt/vep/.vep/loftee_db_${params.assembly}/human_ancestor.fa.gz,conservation_file:/opt/vep/.vep/loftee_db_${params.assembly}/phylocsf_gerp.sql${params.loftee_flags}
bcftools view ${params.drop_genotypes} ${vcf} ${chrom}:${start}-${stop} | vep --cache --offline --assembly ${params.assembly} --format vcf --vcf --compress_output bgzip --force_overwrite --dir_cache /opt/vep/.vep/ --plugin LoF,loftee_path:/opt/vep/.vep/loftee_${params.assembly},\${loftee_args} --dir_plugins /opt/vep/.vep/loftee_${params.assembly} --plugin CADD,/opt/vep/.vep/CADD_${params.assembly}/whole_genome_SNVs.tsv.gz,/opt/vep/.vep/CADD_${params.assembly}/gnomad.genomes-exomes.r4.0.indel.tsv.gz --plugin CONTEXT ${params.vep_flags} --warning_file STDERR --output_file STDOUT > ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.vcf.gz 2> ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.log
sanity_check.py -a ${vcf.getSimpleName()}.${chrom}_${start}_${stop}.vep.vcf.gz
"""
else
error "Invalid assembly name: ${params.assembly}"
}
process concatenate_chunks {
label "VEP"
cache "lenient"
errorStrategy "retry"
maxRetries 3
cpus 1
input:
tuple val(chrom), val(name), path(annotated_vcfs)
output:
tuple val(chrom), val(name), path("${name}.${chrom}.vep.vcf.gz"), path("${name}.${chrom}.vep.vcf.gz.csi")
publishDir "results/vcf", mode: "copy"
"""
for f in ${annotated_vcfs}; do bcftools index \${f}; done
for f in ${annotated_vcfs}; do echo "\${f}"; done | sort -V > files.txt
bcftools concat -a -f files.txt -Oz -o ${name}.${chrom}.vep.vcf.gz
bcftools index ${name}.${chrom}.vep.vcf.gz
"""
}
process summarize {
label "SUMMARY"
cache "lenient"
errorStrategy "retry"
maxRetries 3
cpus 1
input:
tuple val(chrom), val(name), path(vcf), path(vcf_index)
output:
tuple val(name), path("*.summary.txt")
publishDir "results/summary", pattern: "*.summary.txt", mode: "copy"
"""
variant_summary.py -a ${vcf} -o ${name}.${chrom}.summary.txt
"""
}
process concatenate_chromosomes {
label "VEP"
cache "lenient"
cpus 1
input:
tuple val(name), path(vcfs), path(vcf_indices)
output:
tuple path("${name}.vep.vcf.gz"), path("${name}.vep.vcf.gz.csi")
publishDir "results/vcf", mode: "copy"
"""
for f in ${vcfs}; do echo "\${f}"; done | sort -V > files.txt
bcftools concat -a -f files.txt -Oz -o ${name}.vep.vcf.gz
bcftools index ${name}.vep.vcf.gz
"""
}
process notebooks {
label "SUMMARY"
cache "lenient"
executor "local"
cpus 1
input:
tuple val(name), path(summaries)
output:
path "*.html"
publishDir "results/html", pattern: "*.html", mode: "copy"
"""
cp $workflow.projectDir/JNotebooks/*.ipynb .
jupyter nbconvert --to html autosomal_pass.ipynb --output=${name}.auto_pass.html --execute --no-input --ExecutePreprocessor.timeout=1200
jupyter nbconvert --to html autosomal_fail.ipynb --output=${name}.auto_fail.html --execute --no-input --ExecutePreprocessor.timeout=1200
jupyter nbconvert --to html all_pass.ipynb --output=${name}.all_pass.html --execute --no-input --ExecutePreprocessor.timeout=1200
jupyter nbconvert --to html all_fail.ipynb --output=${name}.all_fail.html --execute --no-input --ExecutePreprocessor.timeout=1200
"""
}
workflow {
range = 1..300000000
step = params.window_size
windows = Channel.from(range.by(step)).map { w -> [ w, w + step - 1 ] }
vcfs = Channel.fromPath(params.vcfs).map{ vcf -> [ vcf, vcf + ".tbi" ] }
vcfs_chunks = vcf_by_chrom(vcfs).flatMap({ chroms, vcf, vcf_index -> chroms.split(',').collect { [it, vcf, vcf_index] }}).filter { it[0] =~ /^(chr)?(X|Y|[1-9][0-9]?)$/ }.toSortedList({a, b -> a[0] <=> b[0]}).flatMap({it}).combine(windows)
vcfs_chunks_annotated = annotate_chunks(vcfs_chunks).annotations
vcfs_annotated = concatenate_chunks(vcfs_chunks_annotated.groupTuple(by: [0, 1]))
concatenate_chromosomes(vcfs_annotated.map{ it -> [it[1], it[2], it[3]] }.groupTuple(by: 0))
if (params.enable_summary == true) {
vcfs_summaries = summarize(vcfs_annotated)
notebooks(vcfs_summaries.groupTuple(by: 0))
}
}