Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

stubs and test for rnaseq modules - part IV #5939

Merged
merged 24 commits into from
Jul 12, 2024
Merged

stubs and test for rnaseq modules - part IV #5939

Show file tree
Hide file tree
Changes from 21 commits
Commits
Show all changes
24 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions modules/nf-core/antismash/antismashlite/tests/main.nf.test.snap
View file
Open in desktop
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"
}
}
24 changes: 8 additions & 16 deletions modules/nf-core/antismash/antismashlitedownloaddatabases/tests/main.nf.test.snap
View file
Open in desktop
maxulysse marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
Expand Up @@ -3,38 +3,30 @@
"content": [
{
"0": [
[

]

],
"1": [
[

]

],
"2": [
"versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a"

],
"antismash_dir": [
[

]

],
"database": [
[

]

],
"versions": [
"versions.yml:md5,9eccc775a12d25ca5dfe334e8874f12a"

]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-02-07T23:13:12.85814463"
"timestamp": "2024-07-10T12:41:09.808653"
},
"antiSMASH-lite downloaddatabases": {
"content": [
Expand Down
54 changes: 8 additions & 46 deletions modules/nf-core/bracken/build/tests/main.nf.test.snap
View file
Open in desktop
maxulysse marked this conversation as resolved.
Show resolved Hide resolved
Original file line number Diff line number Diff line change
Expand Up @@ -18,67 +18,29 @@
"content": [
{
"0": [
[
{
"id": "db"
},
[
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]

],
"1": [
[
{
"id": "db"
},
[
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]

],
"2": [
"versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b"

],
"bracken_files": [
[
{
"id": "db"
},
[
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]

],
"db": [
[
{
"id": "db"
},
[
"database.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kmer_distrib:md5,d41d8cd98f00b204e9800998ecf8427e",
"database100mers.kraken:md5,d41d8cd98f00b204e9800998ecf8427e",
"file.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
]
]

],
"versions": [
"versions.yml:md5,925c6ae1387eaf6dbd14656125bc6d9b"

]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.3"
},
"timestamp": "2024-04-17T18:41:14.406736156"
"timestamp": "2024-07-10T13:06:03.38959"
}
}
10 changes: 4 additions & 6 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test
View file
Open in desktop
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() }
)
}

}

}
22 changes: 14 additions & 8 deletions modules/nf-core/centrifuge/centrifuge/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,34 +92,40 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-02-02T07:47:36.886757827"
"timestamp": "2024-07-09T10:36:42.919054"
},
"sarscov2_fastq_se": {
"content": [
"test.report.txt",
"test.results.txt",
"",
""
"",
[
"versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-02-02T08:22:31.470316024"
"timestamp": "2024-07-09T10:36:23.087465"
},
"sarscov2_fastq_pe": {
"content": [
"test.report.txt",
"test.results.txt",
"test.mapped.fastq.1.gz",
"test.unmapped.fastq.1.gz"
"test.unmapped.fastq.1.gz",
[
"versions.yml:md5,1ce028d9f968eca6df31586fe3b77c84"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-02-02T08:22:48.866073154"
"timestamp": "2024-07-09T10:36:33.471335"
}
}
5 changes: 2 additions & 3 deletions modules/nf-core/centrifuge/kreport/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,8 +50,9 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.kreport[0][1]).name,
process.out.versions
).match() }
)
)
}

}
Expand All @@ -75,7 +76,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
13 changes: 8 additions & 5 deletions modules/nf-core/centrifuge/kreport/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,18 +30,21 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-02-02T06:18:36.794405448"
"timestamp": "2024-07-09T10:37:05.883784"
},
"sarscov2_fastq_se": {
"content": [
"test.txt"
"test.txt",
[
"versions.yml:md5,43c766a19f2edf7e05d1a2a0b1816b13"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-02-02T06:28:20.461891873"
"timestamp": "2024-07-09T10:36:53.971559"
}
}
16 changes: 9 additions & 7 deletions modules/nf-core/checkv/updatedatabase/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() },
{ assert snapshot(
"${process.out.checkv_db.get(0).get(1).get(0)}",
"${process.out.checkv_db.get(0).get(1).get(2)}",
Expand All @@ -57,11 +59,10 @@ nextflow_process {
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.faa",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.fna",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.log",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv"
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv",
process.out.versions
).match()
},
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() }
)
}
}
Expand All @@ -84,6 +85,8 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() },
{ assert snapshot(
"${process.out.checkv_db.get(0).get(1).get(0)}",
"${process.out.checkv_db.get(0).get(1).get(2)}",
Expand All @@ -93,11 +96,10 @@ nextflow_process {
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.faa",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.fna",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.log",
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv"
"${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.tsv",
process.out.versions
).match()
},
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd.log").exists() },
{ assert new File("${process.out.checkv_db.get(0).get(1).get(1)}/checkv_reps.dmnd").exists() }
}
)
}
}
Expand Down
22 changes: 18 additions & 4 deletions modules/nf-core/checkv/updatedatabase/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,9 +15,16 @@
"checkv_reps.faa:md5,6f1e81fbab2d6f39367e3a037df1eec9",
"checkv_reps.fna:md5,5f7b89beb65e7405ff2214c2a7c981ba",
"checkv_reps.log:md5,ebd0238f4df0fa5f3a8af40cd2646f84",
"checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c"
"checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c",
[
"versions.yml:md5,e2bdb90d427b1d7b5d3ff4555230cdcd"
]
],
"timestamp": "2024-01-17T17:19:49.436344753"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-09T10:39:34.796067"
},
"sarscov2 - genome - genome_fasta": {
"content": [
Expand All @@ -35,8 +42,15 @@
"checkv_reps.faa:md5,6f1e81fbab2d6f39367e3a037df1eec9",
"checkv_reps.fna:md5,5f7b89beb65e7405ff2214c2a7c981ba",
"checkv_reps.log:md5,ebd0238f4df0fa5f3a8af40cd2646f84",
"checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c"
"checkv_reps.tsv:md5,ccb5c738991f63618ecf9c20c9afa69c",
[
"versions.yml:md5,e2bdb90d427b1d7b5d3ff4555230cdcd"
]
],
"timestamp": "2023-12-11T15:51:27.123218646"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-09T10:39:17.749242"
}
}
8 changes: 3 additions & 5 deletions modules/nf-core/controlfreec/freec/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -70,9 +70,9 @@ nextflow_process {
path(process.out.BAF.get(0).get(1)).readLines()[0],
path(process.out.ratio.get(0).get(1)).readLines()[0],
path(process.out.config.get(0).get(1)).readLines()[0],
path(process.out.info.get(0).get(1)).readLines()[0]
).match() },
{ assert snapshot(process.out.versions).match("version") }
path(process.out.info.get(0).get(1)).readLines()[0],
process.out.versions
).match() }
)
}

Expand Down Expand Up @@ -159,7 +159,5 @@ nextflow_process {
{ assert snapshot(process.out).match() }
)
}

}

}
Loading
Loading