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narfmap cleanup (nf-core#5937)
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* chore: Add Note about issue

* test: Remove bam name

Co-authored-by: maxulysse <[email protected]>

---------

Co-authored-by: maxulysse <[email protected]>
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@edmundmiller @maxulysse
edmundmiller and maxulysse authored Jul 8, 2024
1 parent ccedf37 commit c549fe2
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Showing 4 changed files with 37 additions and 52 deletions.
20 changes: 6 additions & 14 deletions modules/nf-core/narfmap/align/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down Expand Up @@ -87,9 +86,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down Expand Up @@ -134,9 +132,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down Expand Up @@ -181,9 +178,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down Expand Up @@ -228,9 +224,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down Expand Up @@ -276,14 +271,11 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
}

}

}
52 changes: 23 additions & 29 deletions modules/nf-core/narfmap/align/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,24 +10,23 @@
"test.bam:md5,5c407c8e621fc931af17a585526598bf"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:45:10.095839411"
"timestamp": "2024-07-08T12:31:24.171738358"
},
"sarscov2 - [fastq1, fastq2], hashtable, true - stub": {
"content": [
Expand All @@ -41,18 +40,17 @@
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"

],
"test.bam",
[

"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:45:22.364107512"
"timestamp": "2024-07-08T12:31:44.736492735"
},
"sarscov2 - fastq, hashtable, false": {
"content": [
Expand All @@ -65,24 +63,23 @@
"test.bam:md5,ea3a6f419b6c8f91e99603058c608124"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:43:57.96792573"
"timestamp": "2024-07-08T12:19:58.278501718"
},
"sarscov2 - fastq, hashtable, true": {
"content": [
Expand All @@ -95,24 +92,23 @@
"test.bam:md5,e2632fce5442e05210edd516715489c4"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:44:17.486586239"
"timestamp": "2024-07-08T12:20:22.893500585"
},
"sarscov2 - [fastq1, fastq2], hashtable, false": {
"content": [
Expand All @@ -125,24 +121,23 @@
"test.bam:md5,ef0c12ae27778b906fd4f822ef7ce074"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:44:48.178604348"
"timestamp": "2024-07-08T12:20:54.147168602"
},
"sarscov2 - [fastq1, fastq2], hashtable, true": {
"content": [
Expand All @@ -155,23 +150,22 @@
"test.bam:md5,54965e6a11a9c31b1ae3c7e896c96c32"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:44:55.858525101"
"timestamp": "2024-07-08T12:21:06.378368579"
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/narfmap/align/tests/segfault.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@ nextflow_process {
tag "narfmap/hashtable"
tag "bug"

test("This should segfault") {
// https://github.com/bioinformaticsorphanage/NARFMAP/issues/10
test("This should NOT segfault") {

setup {
run("NARFMAP_HASHTABLE") {
Expand Down Expand Up @@ -44,9 +45,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out.bam,
process.out.versions,
file(process.out.bam[0][1]).name,
file(process.out.log[0][1]).readLines().findAll { it.startsWith("decompHash") },
process.out.versions,
).match()
}
)
Expand Down
11 changes: 5 additions & 6 deletions modules/nf-core/narfmap/align/tests/segfault.nf.test.snap
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"This should segfault": {
"This should NOT segfault": {
"content": [
[
[
Expand All @@ -10,23 +10,22 @@
"test.bam:md5,c38463b4da3a56010093cf2ce7634b86"
]
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
],
"test.bam",
[
"decompHashTableCtxInit...",
"decompHashTableHeader...",
"decompHashTableLiterals...",
"decompHashTableExtIndex...",
"decompHashTableAutoHits...",
"decompHashTableSetFlags..."
],
[
"versions.yml:md5,f7f7afeeca9aecd25ef825978aac55d7"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-08T11:46:14.084669293"
"timestamp": "2024-07-08T12:32:26.897477754"
}
}

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