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Added nf-test for biobambam/bamsormadup #6579

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Sep 5, 2024
Merged

Added nf-test for biobambam/bamsormadup #6579

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18 changes: 18 additions & 0 deletions modules/nf-core/biobambam/bamsormadup/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -48,4 +48,22 @@ process BIOBAMBAM_BAMSORMADUP {
bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."

"""
touch ${prefix}.${suffix}
touch ${prefix}.metrics.txt

cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamcat: \$(echo \$(bamcat --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
bamcollate2: \$(echo \$(bamcollate2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS
"""
}
105 changes: 105 additions & 0 deletions modules/nf-core/biobambam/bamsormadup/tests/main.nf.test
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@@ -0,0 +1,105 @@

nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "biobambam"
tag "biobambam/bamsormadup"

test("test-biobambam-bamsormadup-multi-input") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true)
]
]
input[1] = [[:],[]]

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.bam_index,
process.out.cram,
file(process.out.metrics[0][1]).readLines()[3..5],
process.out.versions
).match()
}
)
}
}

test("test-biobambam-bamsormadup-single-input") {

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
]
]
input[1] = [[:],[]]

"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.bam_index,
process.out.cram,
file(process.out.metrics[0][1]).readLines()[3..5],
process.out.versions
).match()
}
)
}
}

test("test-biobambam-bamsormadup-single-input-stub") {

options '-stub'

when {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
]
]
input[1] = [[:],[]]

"""
}
}

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

}
115 changes: 115 additions & 0 deletions modules/nf-core/biobambam/bamsormadup/tests/main.nf.test.snap
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@@ -0,0 +1,115 @@
{
"test-biobambam-bamsormadup-single-input": {
"content": [
"e296148e4f68882cc91fb624e392f539",
[

],
[

],
[
"LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE",
"lib1\t3\t97\t3\t0\t0\t0\t0\t-1",
""
],
[
"versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-05T22:00:39.772883"
},
"test-biobambam-bamsormadup-multi-input": {
"content": [
"3dc03384b330e3f16e15691c9189e890",
[

],
[

],
[
"LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE",
"lib1\t3\t97\t3\t0\t0\t0\t0\t-1",
"testN\t0\t2820\t2\t0\t828\t0\t0.293617\t3807"
],
[
"versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-05T22:00:31.187999"
},
"test-biobambam-bamsormadup-single-input-stub": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [

],
"2": [

],
"3": [
[
{
"id": "test",
"single_end": false
},
"test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"4": [
"versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
],
"bam": [
[
{
"id": "test",
"single_end": false
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"bam_index": [

],
"cram": [

],
"metrics": [
[
{
"id": "test",
"single_end": false
},
"test.metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,67ab301f20567acd9d0e648c2a3e158c"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-05T21:57:13.430982"
}
}
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Expand Up @@ -52,9 +52,6 @@ bedtools/intersect:
bedtools/unionbedg:
- modules/nf-core/bedtools/unionbedg/**
- tests/modules/nf-core/bedtools/unionbedg/**
biobambam/bamsormadup:
- modules/nf-core/biobambam/bamsormadup/**
- tests/modules/nf-core/biobambam/bamsormadup/**
biohansel:
- modules/nf-core/biohansel/**
- tests/modules/nf-core/biohansel/**
Expand Down
25 changes: 0 additions & 25 deletions tests/modules/nf-core/biobambam/bamsormadup/main.nf
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5 changes: 0 additions & 5 deletions tests/modules/nf-core/biobambam/bamsormadup/nextflow.config
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23 changes: 0 additions & 23 deletions tests/modules/nf-core/biobambam/bamsormadup/test.yml
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