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update vcfeval inputs + nf-test conversion #6714

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Sep 30, 2024
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update vcfeval inputs + nf-test conversion #6714

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4 changes: 2 additions & 2 deletions modules/nf-core/rtgtools/rocplot/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -35,8 +35,8 @@ nextflow_process {
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true)
]
input[1] = UNTAR.out.untar
println(projectDir)
Expand Down
20 changes: 10 additions & 10 deletions modules/nf-core/rtgtools/vcfeval/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ process RTGTOOLS_VCFEVAL {
'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"

input:
tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(evaluation_bed)
tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(regions_bed)
tuple val(meta2), path(sdf)

output:
Expand All @@ -33,8 +33,8 @@ process RTGTOOLS_VCFEVAL {
script:
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
def bed_regions = truth_bed ? "--bed-regions=${truth_bed}" : ""
def eval_regions = evaluation_bed ? "--evaluation-regions=${evaluation_bed}" : ""
def bed_regions = regions_bed ? "--bed-regions=${regions_bed}" : ""
def eval_regions = truth_bed ? "--evaluation-regions=${truth_bed}" : ""
def truth_index = truth_vcf_tbi ? "" : "rtg index ${truth_vcf}"
def query_index = query_vcf_tbi ? "" : "rtg index ${query_vcf}"
def avail_mem = task.memory.toGiga() + "G"
Expand Down Expand Up @@ -68,17 +68,17 @@ process RTGTOOLS_VCFEVAL {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.tp.vcf.gz
echo | gzip > ${prefix}.tp.vcf.gz
touch ${prefix}.tp.vcf.gz.tbi
touch ${prefix}.fn.vcf.gz
echo | gzip > ${prefix}.fn.vcf.gz
touch ${prefix}.fn.vcf.gz.tbi
touch ${prefix}.fp.vcf.gz
echo | gzip > ${prefix}.fp.vcf.gz
touch ${prefix}.fp.vcf.gz.tbi
touch ${prefix}.tp-baseline.vcf.gz
echo | gzip > ${prefix}.tp-baseline.vcf.gz
touch ${prefix}.tp-baseline.vcf.gz.tbi
touch ${prefix}.snp_roc.tsv.gz
touch ${prefix}.non_snp_roc.tsv.gz
touch ${prefix}.weighted_roc.tsv.gz
echo | gzip > ${prefix}.snp_roc.tsv.gz
echo | gzip > ${prefix}.non_snp_roc.tsv.gz
echo | gzip > ${prefix}.weighted_roc.tsv.gz
touch ${prefix}.summary.txt
touch ${prefix}.phasing.txt

Expand Down
4 changes: 3 additions & 1 deletion modules/nf-core/rtgtools/vcfeval/meta.yml
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Expand Up @@ -40,11 +40,13 @@ input:
type: file
description: A BED file containining the strict regions where VCFeval should
only evaluate the fully overlapping variants (optional)
This input should be used to provide the golden truth BED files.
pattern: "*.bed"
- evaluation_bed:
- regions_bed:
type: file
description: A BED file containing the regions where VCFeval will evaluate every
fully and partially overlapping variant (optional)
This input should be used to provide the regions used by the analysis
pattern: "*.bed"
- - meta2:
type: map
Expand Down
113 changes: 113 additions & 0 deletions modules/nf-core/rtgtools/vcfeval/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,113 @@
nextflow_process {

name "Test Process RTGTOOLS_VCFEVAL"
script "../main.nf"
process "RTGTOOLS_VCFEVAL"

tag "modules"
tag "modules_nfcore"
tag "rtgtools"
tag "rtgtools/vcfeval"
tag "untar"

setup {
run("UNTAR") {
script "../../../untar/main.nf"
process {
"""
input[0] = Channel.value([
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz', checkIfExists:true)
])
"""
}
}
}

test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf") {

when {
process {
"""
input[0] = Channel.of([
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true)
])
input[1] = UNTAR.out.untar
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo_sapiens - [vcf, [], truth, [], [], []], sdf") {

when {
process {
"""
input[0] = Channel.of([
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true),
[],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true),
[],
[],
[]
])
input[1] = UNTAR.out.untar
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub") {

options "-stub"

when {
process {
"""
input[0] = Channel.of([
[id:'test'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true)
])
input[1] = UNTAR.out.untar
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}

}

}
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