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stubs and test for rnaseq modules - part IV #5939

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merged 24 commits into from
Jul 12, 2024
Merged

stubs and test for rnaseq modules - part IV #5939

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d292234
fix stubs and add stub tests
maxulysse Jul 9, 2024
6fec892
fix linting
maxulysse Jul 9, 2024
5eacdc3
fix some linting
maxulysse Jul 9, 2024
06d1663
fix linting
maxulysse Jul 9, 2024
2b570f9
better comment
maxulysse Jul 9, 2024
15697e8
change container
maxulysse Jul 10, 2024
a4edbd1
update snapshots
maxulysse Jul 10, 2024
7963390
improve untar stubs
maxulysse Jul 10, 2024
22eeb88
Merge branch 'master' into stubs_rnaseq_viii
maxulysse Jul 10, 2024
45cc921
update snapshots
maxulysse Jul 10, 2024
6e5b70f
update snapshots
maxulysse Jul 10, 2024
0181665
update env
maxulysse Jul 10, 2024
4ca951f
Merge branch 'master' into stubs_rnaseq_viii
maxulysse Jul 11, 2024
a66b5cd
better
maxulysse Jul 11, 2024
1469a02
use seqera containers
maxulysse Jul 11, 2024
8f5f2f5
Merge branch 'master' into stubs_rnaseq_viii
maxulysse Jul 11, 2024
3610d03
quay.io
maxulysse Jul 11, 2024
a5f46e7
proper usage
maxulysse Jul 11, 2024
7bbd0f3
Merge branch 'master' into stubs_rnaseq_viii
maxulysse Jul 11, 2024
bb9e0f9
update snapshots
maxulysse Jul 11, 2024
7a2e68d
keep ubuntu for now
maxulysse Jul 12, 2024
c0790db
update tests and snap
maxulysse Jul 12, 2024
ceb4a8f
update test and snapshot
maxulysse Jul 12, 2024
ef67963
update test and snapshot
maxulysse Jul 12, 2024
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4 changes: 2 additions & 2 deletions modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -294,8 +294,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-02-09T17:06:15.671842533"
"timestamp": "2024-07-11T16:35:51.079804"
}
}
111 changes: 74 additions & 37 deletions modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,46 +10,47 @@ nextflow_process {
tag "antismash/antismashlitedownloaddatabases"
tag "untar"

setup {
test("antiSMASH-lite downloaddatabases") {

run("UNTAR", alias: "UNTAR_CSS") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
"""
setup {

run("UNTAR", alias: "UNTAR_CSS") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
"""
}
}
}

run("UNTAR", alias: "UNTAR_DETECTION") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
"""
run("UNTAR", alias: "UNTAR_DETECTION") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
"""
}
}
}

run("UNTAR", alias: "UNTAR_MODULES") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
"""
run("UNTAR", alias: "UNTAR_MODULES") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
"""
}
}
}
}

test("antiSMASH-lite downloaddatabases") {
when {
process {
"""
Expand All @@ -64,18 +65,56 @@ test("antiSMASH-lite downloaddatabases") {
assertAll(
{ assert process.success },
{ assert snapshot (
file(process.out.database.get(0)).list().sort(),
process.out.versions,
file(process.out.database.get(0)).list().sort(),
process.out.versions,
).match() }
)
}

}

test("antiSMASH-lite downloaddatabases - stub") {

options "-stub"

setup {

run("UNTAR", alias: "UNTAR_CSS") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
"""
}
}

run("UNTAR", alias: "UNTAR_DETECTION") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
"""
}
}

run("UNTAR", alias: "UNTAR_MODULES") {
script "modules/nf-core/untar/main.nf"
process {
"""
input[0] = [
[ ],
file('https://github.com/nf-core/test-datasets/raw/59ddeb5929f89ddddaff292d67f9025812762b87/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
"""
}
}
}

when {
process {
"""
Expand All @@ -92,7 +131,5 @@ test("antiSMASH-lite downloaddatabases") {
{ assert snapshot(process.out).match() }
)
}

}

}
8 changes: 4 additions & 4 deletions modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,9 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-02-07T23:13:12.85814463"
"timestamp": "2024-07-12T13:41:29.456143"
},
"antiSMASH-lite downloaddatabases": {
"content": [
Expand All @@ -55,8 +55,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-02-07T23:12:29.947339678"
"timestamp": "2024-07-12T13:41:08.116244"
}
}
34 changes: 22 additions & 12 deletions modules/nf-core/bracken/build/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -10,18 +10,18 @@ nextflow_process {
tag "bracken/build"
tag "untar"

setup {
run ("UNTAR") {
script "../../../untar/main.nf"
process {
"""
input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
"""
test("kraken2 - db") {

setup {
run ("UNTAR") {
script "../../../untar/main.nf"
process {
"""
input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
"""
}
}
}
}

test("kraken2 - db") {

when {
process {
Expand All @@ -41,6 +41,7 @@ nextflow_process {
file("${process.out.bracken_files[0][1]}/database100mers.kmer_distrib").name,
file("${process.out.bracken_files[0][1]}/database100mers.kraken").name,
file("${process.out.bracken_files[0][1]}/database.kraken").name,
process.out.versions
).match()
}
)
Expand All @@ -52,6 +53,17 @@ nextflow_process {

options "-stub"

setup {
run ("UNTAR") {
script "../../../untar/main.nf"
process {
"""
input[0] = [[id: 'db'],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2_intermediate.tar.gz', checkIfExists: true)]
"""
}
}
}

when {
process {
"""
Expand All @@ -66,7 +78,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
59 changes: 52 additions & 7 deletions modules/nf-core/bracken/build/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,16 @@
"database.kraken",
"database100mers.kmer_distrib",
"database100mers.kraken",
"database.kraken"
"database.kraken",
[
"versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-04-17T18:41:03.693430543"
"timestamp": "2024-07-12T13:45:17.37462"
},
"kraken2 - db - stub": {
"content": [
Expand All @@ -26,7 +29,28 @@
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
[
[
"G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
"G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
"z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
"seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e",
"taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
"nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
"nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
Expand Down Expand Up @@ -66,7 +90,28 @@
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
"hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
[
[
"G46z5ZvKEd.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
"G46z5ZvKEd.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map_MtGz4nUfR3.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map_eNakvrOVZm.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"z_4A5lulyr.fna:md5,d41d8cd98f00b204e9800998ecf8427e",
"z_4A5lulyr.fna.masked:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
"seqid2taxid.map:md5,d41d8cd98f00b204e9800998ecf8427e",
"taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e",
[
"names.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
"nodes.dmp:md5,d41d8cd98f00b204e9800998ecf8427e",
"nucl_gb.accession2taxid:md5,d41d8cd98f00b204e9800998ecf8427e",
"prelim_map.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"unmapped.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]
],
Expand All @@ -77,8 +122,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-04-17T18:41:14.406736156"
"timestamp": "2024-07-12T13:45:26.452181"
}
}
10 changes: 4 additions & 6 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -42,10 +42,10 @@ nextflow_process {
file(process.out.results[0][1]).name,
file(process.out.fastq_mapped[0][1][0]).name,
file(process.out.fastq_unmapped[0][1][0]).name,
process.out.versions
).match() }
)
}

}

test("sarscov2_fastq_pe") {
Expand All @@ -56,8 +56,8 @@ nextflow_process {
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
input[1] = UNTAR.out.untar.map{ it[1] }
input[2] = true
input[3] = true
Expand All @@ -73,10 +73,10 @@ nextflow_process {
file(process.out.results[0][1]).name,
file(process.out.fastq_mapped[0][1][0]).name,
file(process.out.fastq_unmapped[0][1][0]).name,
process.out.versions
).match() }
)
}

}

test("sarscov2_fastq_se_stub") {
Expand All @@ -100,7 +100,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
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