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Convert ultraplex to nf-test #5706

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Convert ultraplex to nf-test #5706

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2d942f7
Convert ultraplex to nf-test
SPPearce May 28, 2024
8ddfa0c
Add mv command to rename the matching files to be able to filter out …
SPPearce Jun 5, 2024
6156c4e
Merge branch 'master' into ultraplex
SPPearce Jun 5, 2024
73561f8
Update modules/nf-core/ultraplex/main.nf
SPPearce Jun 5, 2024
2f46003
Add prefix and update stub
SPPearce Jun 5, 2024
db4369c
Remove optional value input, refactor, bump versions
SPPearce Jun 5, 2024
eeeb103
Merge branch 'master' into ultraplex
SPPearce Aug 20, 2024
9781a75
Merge branch 'master' into ultraplex
SPPearce Sep 18, 2024
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33 changes: 29 additions & 4 deletions modules/nf-core/ultraplex/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,10 @@ process ULTRAPLEX {
val(adapter_seq)

output:
tuple val(meta), path("*[!no_match].fastq.gz"), emit: fastq
tuple val(meta), path("*no_match.fastq.gz"), optional: true, emit: no_match_fastq
path "*.log", emit: report
path "versions.yml", emit: versions
tuple val(meta), path("*matched.fastq.gz") , emit: fastq
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tuple val(meta), path("*no_match.fastq.gz"), emit: no_match_fastq, optional: true
path "*.log" , emit: report
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
Expand Down Expand Up @@ -47,6 +47,31 @@ process ULTRAPLEX {

"""
${ultraplex_command}

## rename the matched files to be able to emit only the matched files
MATCHES=\$( find . -type f -name '*.fastq.gz' ! -name '*_no_match_*.fastq.gz' )
for MATCH in \$MATCHES; do
mv \$MATCH \${MATCH/.fastq.gz/_matched.fastq.gz}
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done

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ultraplex: $VERSION
END_VERSIONS
"""

stub:
def VERSION = "1.2.5" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ultraplex_demux_Sample1_matched.fastq.gz
echo "" | gzip > ultraplex_demux_Sample2_matched.fastq.gz
echo "" | gzip > ultraplex_demux_Sample1_no_match.fastq.gz
echo "" | gzip > ultraplex_demux_Sample2_no_match.fastq.gz

touch ultraplex.log

cat <<-END_VERSIONS > versions.yml
"${task.process}":
ultraplex: $VERSION
Expand Down
148 changes: 148 additions & 0 deletions modules/nf-core/ultraplex/tests/main.nf.test
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Original file line number Diff line number Diff line change
@@ -0,0 +1,148 @@
nextflow_process {

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

tag "modules"
tag "modules_nfcore"
tag "ultraplex"

test("ultraplex") {

when {
process {
"""
input[0] = [[id: "test"],
file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/multiplexed.fastq.gz", checkIfExists: true)
]
input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/barcodes.csv", checkIfExists: true)
input[2] = ""
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.no_match_fastq,
process.out.versions).match()},
{ assert process.out.report.get(0) ==~ ".*ultraplex_.*.log" }
)

}

}

test("ultraplex - adaptor") {

when {
process {
"""
input[0] = [[id: "test"],
file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/multiplexed.fastq.gz", checkIfExists: true)
]
input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/barcodes.csv", checkIfExists: true)
input[2] = "AGATCGGAAGAGCGGTTCAG"
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.no_match_fastq,
process.out.versions).match()},
{ assert process.out.report.get(0) ==~ ".*ultraplex_.*.log" }
)
}

}

test("ultraplex - pairedend") {

when {
process {
"""
input[0] = [[id: "test"],
[file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/multiplexed.fastq.gz", checkIfExists: true),
file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/multiplexed2.fastq.gz", checkIfExists: true)]
]
input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/barcodes.csv", checkIfExists: true)
input[2] = ""
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.no_match_fastq,
process.out.versions).match()},
{ assert process.out.report.get(0) ==~ ".*ultraplex_.*.log" }
)
}

}

test("ultraplex - incorrect barcodes") {

when {
process {
"""
input[0] = [[id: "test"],
[ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ]
]
input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/barcodes.csv", checkIfExists: true)
input[2] = ""
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.fastq,
process.out.no_match_fastq,
process.out.versions).match()},
{ assert process.out.report.get(0) ==~ ".*ultraplex_.*.log" }
)
}

}


test("ultraplex - stub") {

options "-stub"

when {
process {
"""
input[0] = [[id: "test"],
file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/reads/multiplexed.fastq.gz", checkIfExists: true)
]
input[1] = file("https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/barcodes.csv", checkIfExists: true)
input[2] = ""
"""
}
}

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

}

}
175 changes: 175 additions & 0 deletions modules/nf-core/ultraplex/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -0,0 +1,175 @@
{
"ultraplex - incorrect barcodes": {
"content": [
[
[
{
"id": "test"
},
[
"ultraplex_demux_Sample2_Fwd_matched.fastq.gz:md5,4451dd878b7d12ff8ceb05fce2ebfa89",
"ultraplex_demux_Sample2_Rev_matched.fastq.gz:md5,f1c6ca8d7f8407b5bb0b6e8906fe41ad"
]
]
],
[

],
[
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-05T06:08:12.106448378"
},
"ultraplex - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_matched.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"ultraplex_demux_Sample2_matched.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"1": [
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_no_match.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"ultraplex_demux_Sample2_no_match.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"2": [
"ultraplex.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"3": [
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
],
"fastq": [
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_matched.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"ultraplex_demux_Sample2_matched.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"no_match_fastq": [
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_no_match.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"ultraplex_demux_Sample2_no_match.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
"report": [
"ultraplex.log:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"versions": [
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-05T05:52:36.211334997"
},
"ultraplex - adaptor": {
"content": [
[
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_matched.fastq.gz:md5,77870ddf54ed3e474d4bb63fea65fc08",
"ultraplex_demux_Sample2_matched.fastq.gz:md5,f3960ec2757672915538923ecb3539f8"
]
]
],
[

],
[
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-05T05:54:27.606493007"
},
"ultraplex": {
"content": [
[
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_matched.fastq.gz:md5,77870ddf54ed3e474d4bb63fea65fc08",
"ultraplex_demux_Sample2_matched.fastq.gz:md5,f3960ec2757672915538923ecb3539f8"
]
]
],
[

],
[
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-05T05:54:11.263761896"
},
"ultraplex - pairedend": {
"content": [
[
[
{
"id": "test"
},
[
"ultraplex_demux_Sample1_Fwd_matched.fastq.gz:md5,6b516012c4b19bb0d2109881e3a36102",
"ultraplex_demux_Sample1_Rev_matched.fastq.gz:md5,79637dfeca38bc9314cc5bde37373b5f",
"ultraplex_demux_Sample2_Fwd_matched.fastq.gz:md5,1f17530c291f74a6b29c63ebaba15c96",
"ultraplex_demux_Sample2_Rev_matched.fastq.gz:md5,81ea922ee9842b8f6fe9654406b4f479"
]
]
],
[

],
[
"versions.yml:md5,916995657ca9c5fd70171d69c3aba409"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-06-05T05:54:44.157822884"
}
}
2 changes: 2 additions & 0 deletions modules/nf-core/ultraplex/tests/tags.yml
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@@ -0,0 +1,2 @@
ultraplex:
- "modules/nf-core/ultraplex/**"
3 changes: 0 additions & 3 deletions tests/config/pytest_modules.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -1902,9 +1902,6 @@ ultra/index:
ultra/pipeline:
- modules/nf-core/ultra/pipeline/**
- tests/modules/nf-core/ultra/pipeline/**
ultraplex:
- modules/nf-core/ultraplex/**
- tests/modules/nf-core/ultraplex/**
umitools/group:
- modules/nf-core/umitools/group/**
- tests/modules/nf-core/umitools/group/**
Expand Down
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