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Merged
LouisLeNezet merged 7 commits into from
Mar 24, 2025
Merged

Migrate BAMTOOLS/CONVERT to nf-test #7958

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c7dca3f
Migrate to nf-test
LouisLeNezet Mar 24, 2025
f70e649
Update modules/nf-core/bamtools/convert/main.nf
LouisLeNezet Mar 24, 2025
0fb9587
Update modules/nf-core/bamtools/convert/tests/main.nf.test
LouisLeNezet Mar 24, 2025
cce7415
Update modules/nf-core/bamtools/convert/tests/main.nf.test
LouisLeNezet Mar 24, 2025
f2c04fa
Update modules/nf-core/bamtools/convert/tests/main.nf.test
LouisLeNezet Mar 24, 2025
7bd9459
Update variable names
LouisLeNezet Mar 24, 2025
019ea1e
Fix spacing
LouisLeNezet Mar 24, 2025
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29 changes: 22 additions & 7 deletions modules/nf-core/bamtools/convert/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -18,23 +18,38 @@ process BAMTOOLS_CONVERT {
task.ext.when == null || task.ext.when

script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def test = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
if ( test == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"
m = args =~ /-format ([a-z]+)/
ext = m[0][1]
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
format_cmd = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
matched_format = args =~ /-format ([a-z]+)/
extension = matched_format[0][1]
if ( format_cmd == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"

"""
bamtools \\
convert \\
$args \\
-in $bam \\
-out ${prefix}.${ext}
-out ${prefix}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
format_cmd = args ==~ /-format (bed|fasta|fastq|json|pileup|sam|yaml)/
matched_format = args =~ /-format ([a-z]+)/
extension = matched_format[0][1]
if ( format_cmd == false ) error "-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml"

"""
touch ${prefix}.${extension}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamtools: \$( bamtools --version | grep -e 'bamtools' | sed 's/^.*bamtools //' )
END_VERSIONS
"""
}
233 changes: 233 additions & 0 deletions modules/nf-core/bamtools/convert/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,233 @@
nextflow_process {

name "Test Process BAMTOOLS_CONVERT"
config "./nextflow.config"
script "../main.nf"
process "BAMTOOLS_CONVERT"

tag "modules"
tag "modules_nfcore"
tag "bamtools"
tag "bamtools/convert"

test("test_bamtools_convert_ext_error") {
when {
params {
module_args = "-format vcf"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.failed },
{ assert process.errorReport.contains("-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml") }
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)
}
}
test("test_bamtools_convert_noext_error") {
when {
params {
module_args = ""
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.failed },
{ assert process.errorReport.contains("-format option must be provided in args. Possible values: bed fasta fastq json pileup sam yaml") }
)
}
}
test("test_bamtools_convert_bed") {
when {
params {
module_args = "-format bed"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_fasta") {
when {
params {
module_args = "-format fasta"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_fastq") {
when {
params {
module_args = "-format fastq"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_json") {


when {
params {
module_args = "-format json"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_pileup") {


when {
params {
module_args = "-format pileup"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_sam") {


when {
params {
module_args = "-format sam"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
test("test_bamtools_convert_yaml") {
when {
params {
module_args = "-format yaml"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("test_bamtools_convert_yaml - stub") {
when {
params {
module_args = "-format yaml"
}
process {
"""
input[0] = [
[id:'test', single_end:false],
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
process.out.versions.collect{path(it).yaml}
).match() }
)
}
}
}
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