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Don't use test scripts when the -fisher option has been given in vardictjava #6747

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merged 2 commits into from
Oct 7, 2024
+152 −18
Merged

Don't use test scripts when the -fisher option has been given in vardictjava #6747

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398e2b1
add option to run --fisher for vardict
nvnieuwk Oct 7, 2024
f9bfe71
use a check for the `-fisher` arg instead
nvnieuwk Oct 7, 2024
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12 changes: 6 additions & 6 deletions modules/nf-core/vardictjava/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process VARDICTJAVA {

output:
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -25,9 +25,12 @@ process VARDICTJAVA {
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

// Don't run test scripts when -fisher has been used by vardictjava
def run_test = !args.contains("-fisher")

def somatic = bams instanceof List && bams.size() == 2 ? true : false
def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}"
def filter = somatic ? "testsomatic.R" : "teststrandbias.R"
def test = run_test ? somatic ? "| testsomatic.R" : "| teststrandbias.R" : ""
def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl"
"""
export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=${fasta}"'
Expand All @@ -37,7 +40,7 @@ process VARDICTJAVA {
-th ${task.cpus} \\
-G ${fasta} \\
${bed} \\
| ${filter} \\
${test} \\
| ${convert_to_vcf} \\
${args2} \\
| bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz
Expand All @@ -50,9 +53,6 @@ process VARDICTJAVA {
"""

stub:
def args = task.ext.args ?: '-c 1 -S 2 -E 3'
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand Down
77 changes: 71 additions & 6 deletions modules/nf-core/vardictjava/tests/main.nf.test
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Expand Up @@ -10,9 +10,6 @@ nextflow_process {
test("homo_sapiens - [bam, bai, bed] - fasta - fai") {

when {
params {
outdir = $outputDir
}
process {
"""
input[0] = Channel.value([
Expand Down Expand Up @@ -47,9 +44,6 @@ nextflow_process {
test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai") {

when {
params {
outdir = $outputDir
}
process {
"""
input[0] = Channel.value([
Expand Down Expand Up @@ -87,4 +81,75 @@ nextflow_process {

}

test("homo_sapiens - [bam, bai, bed] - fasta - fai - fisher") {

config "./nextflow.config"
when {
process {
"""
input[0] = Channel.value([
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
])
input[1] = [
[id:"ref"],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[id:"ref"],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
"""
}
}

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


}

}

test("homo_sapiens - [bam, bai, bed] - fasta - fai - stub") {

options "-stub"

when {
process {
"""
input[0] = Channel.value([
[ id:'test' ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
])
input[1] = [
[id:"ref"],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
]
input[2] = [
[id:"ref"],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
]
"""
}
}

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


}

}

}
78 changes: 72 additions & 6 deletions modules/nf-core/vardictjava/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-04T19:08:38.328190023"
"timestamp": "2024-10-07T16:05:15.117453312"
},
"homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": {
"content": [
Expand Down Expand Up @@ -60,9 +60,75 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-04T19:08:54.416661915"
"timestamp": "2024-10-07T16:05:26.932438089"
},
"homo_sapiens - [bam, bai, bed] - fasta - fai - fisher": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
]
],
"1": [
"versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
]
],
"versions": [
"versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-07T16:05:38.456816851"
},
"homo_sapiens - [bam, bai, bed] - fasta - fai - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"1": [
"versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
],
"vcf": [
[
{
"id": "test"
},
"test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-07T16:05:48.440804849"
}
}
3 changes: 3 additions & 0 deletions modules/nf-core/vardictjava/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
process {
ext.args = "-c 1 -S 2 -E 3 -fisher"
}
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