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Fix bcftools plugin split #5942

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merged 1 commit into from
Jul 10, 2024
Merged

Fix bcftools plugin split #5942

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20 changes: 14 additions & 6 deletions modules/nf-core/bcftools/pluginsplit/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,10 @@ process BCFTOOLS_PLUGINSPLIT {
path(targets)

output:
tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}") , emit: vcf
path "versions.yml" , emit: versions
tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
tuple val(meta), path("*.tbi") , emit: tbi, optional: true
tuple val(meta), path("*.csi") , emit: csi, optional: true
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -32,6 +34,7 @@ process BCFTOOLS_PLUGINSPLIT {

"""
bcftools plugin split \\
${args} \\
${vcf} \\
${samples_arg} \\
${groups_arg} \\
Expand All @@ -56,12 +59,17 @@ process BCFTOOLS_PLUGINSPLIT {
args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
"vcf"

def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
args.contains("--write-index") || args.contains("-W") ? "csi" :
""
def determination_file = samples ?: targets
def create_cmd = extension.matches("vcf|bcf") ? "touch " : "echo '' | gzip > "
def create_files = "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt; while IFS= read -r filename; do ${create_cmd} \"\$filename\"; done < files.txt"
def create_index = index.matches("csi|tbi") ? "cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}.${index}/' > indices.txt; touch \$(<indices.txt)" : ""
"""
cut -f 3 ${determination_file} | sed -e 's/\$/.${extension}/' > files.txt

touch \$(<files.txt)
${create_files}
${create_index}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
192 changes: 192 additions & 0 deletions modules/nf-core/bcftools/pluginsplit/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,192 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "bcftools"
tag "bcftools/pluginsplit"

test("homo_sapiens - [ vcf, tbi ], samples, [], [], []") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[2] = []
input[3] = []
input[4] = []
"""
}
}

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

}

test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = []
input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
"""
}
}

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

)
}

}

test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi") {

config "./nextflow.config"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = []
input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.vcf,
process.out.tbi.get(0).get(1).find { file(it).name.matches("normal.vcf.gz.tbi|tumor.vcf.gz.tbi") },
) }
)
}

}

test("homo_sapiens - [ vcf, tbi ], samples, [], [], [] -stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[2] = []
input[3] = []
input[4] = []
"""
}
}

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

}

test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets -stub") {

options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = []
input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
"""
}
}

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

}

test("homo_sapiens - [ vcf, tbi ], [], groups, regions, targets - tbi -stub") {

config "./nextflow.config"
options "-stub"

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi', checkIfExists: true)
]
input[1] = []
input[2] = Channel.of("normal\t-\tnormal", "tumour\t-\ttumour")
.collectFile(name:"samples.txt", newLine:true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true)
input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.multi_intervals.bed', checkIfExists: true)
"""
}
}

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

}
}
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