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Fix fq/generate #6610

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merged 2 commits into from
Sep 10, 2024
Merged

Fix fq/generate #6610

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91ae8bc
Update snapshot, add stub
SPPearce Sep 6, 2024
ec0ef03
Merge branch 'master' into fq_update
SPPearce Sep 6, 2024
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12 changes: 12 additions & 0 deletions modules/nf-core/fq/generate/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,16 @@ process FQ_GENERATE {
fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g'))
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo | gzip > ${prefix}_R1.fastq.gz
echo | gzip > ${prefix}_R2.fastq.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g'))
END_VERSIONS
"""
}
23 changes: 20 additions & 3 deletions modules/nf-core/fq/generate/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,28 @@ nextflow_process {
tag "fq"
tag "fq/generate"

test("test_fq_lint_fail") {
test("test fq") {
config "./nextflow.config"
when {
params {
outdir = "$outputDir"
process {
"""
input[0] = Channel.of( [ id:'test', single_end:false ] )
"""
}
}

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

}

test("test fq -stub") {
options "-stub"
when {
process {
"""
input[0] = Channel.of( [ id:'test', single_end:false ] )
Expand All @@ -30,4 +46,5 @@ nextflow_process {
}

}

}
57 changes: 51 additions & 6 deletions modules/nf-core/fq/generate/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"test_fq_lint_fail": {
"test fq -stub": {
"content": [
{
"0": [
Expand All @@ -9,8 +9,8 @@
"single_end": false
},
[
"test_R1.fastq.gz:md5,1d262f7028e65d291c4a46f890f539e1",
"test_R2.fastq.gz:md5,d7bd728bb013edced318e2a797ad60b3"
"test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
Expand All @@ -24,8 +24,8 @@
"single_end": false
},
[
"test_R1.fastq.gz:md5,1d262f7028e65d291c4a46f890f539e1",
"test_R2.fastq.gz:md5,d7bd728bb013edced318e2a797ad60b3"
"test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
"test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
]
],
Expand All @@ -34,6 +34,51 @@
]
}
],
"timestamp": "2023-10-17T11:27:57.943374"
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-06T16:03:12.733228308"
},
"test fq": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
},
[
"test_R1.fastq.gz:md5,3acdc5cb66c65a6fb1e8a87c37dec288",
"test_R2.fastq.gz:md5,026a0d0711dc3cd581ab26c5b1757eee"
]
]
],
"1": [
"versions.yml:md5,def2d5900b648a4fc802b237e985efb7"
],
"fastq": [
[
{
"id": "test",
"single_end": false
},
[
"test_R1.fastq.gz:md5,3acdc5cb66c65a6fb1e8a87c37dec288",
"test_R2.fastq.gz:md5,026a0d0711dc3cd581ab26c5b1757eee"
]
]
],
"versions": [
"versions.yml:md5,def2d5900b648a4fc802b237e985efb7"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-06T16:03:01.858857277"
}
}
5 changes: 1 addition & 4 deletions modules/nf-core/fq/generate/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,8 +1,5 @@
process {

publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }

withName: FQ_GENERATE {
ext.args = '-s 123'
}
}
}
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