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Fix conda tests
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@nschcolnicov
nschcolnicov committed Dec 11, 2024
1 parent 22db11c commit e54ce38
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Showing 8 changed files with 147 additions and 263 deletions.
8 changes: 6 additions & 2 deletions modules/nf-core/custom/matrixfilter/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,9 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.filtered).match("filtered") },
{ assert snapshot(process.out.tests).match("tests") },
{ assert snapshot(process.out.versions).match("versions") }
)
}
}
Expand All @@ -46,7 +48,9 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.filtered).match("filtered_stub") },
{ assert snapshot(process.out.tests).match("tests_stub") },
{ assert snapshot(process.out.versions).match("versions_stub") }
)
}
}
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192 changes: 77 additions & 115 deletions modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,132 +1,94 @@
{
"test_custom_matrixfilter": {
"filtered_stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66"
]
],
"1": [
[
{
"id": "test"
},
"test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2"
]
],
"2": [
[
{
"id": "test"
},
"R_sessionInfo.log:md5,e19eea53ec9086b4ac47332e354c4cc1"
]
],
"3": [
"versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
],
"filtered": [
[
{
"id": "test"
},
"test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66"
]
],
"session_info": [
[
{
"id": "test"
},
"R_sessionInfo.log:md5,e19eea53ec9086b4ac47332e354c4cc1"
]
],
"tests": [
[
{
"id": "test"
},
"test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2"
]
],
"versions": [
"versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
[
[
{
"id": "test"
},
"mock.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T19:46:57.516473857"
"timestamp": "2024-12-11T20:24:23.270885558"
},
"test_custom_matrixfilter - stub": {
"versions_stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"mock.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"mock.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
[
{
"id": "test"
},
"R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"3": [
"versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
],
"filtered": [
[
{
"id": "test"
},
"mock.filtered.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"session_info": [
[
{
"id": "test"
},
"R_sessionInfo.log:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"tests": [
[
{
"id": "test"
},
"mock.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
[
"versions.yml:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T20:24:23.286233277"
},
"tests": {
"content": [
[
[
{
"id": "test"
},
"test.tests.tsv:md5,9a0f14988df8c1b8975039eed91b85e2"
]
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T20:24:15.105582542"
},
"tests_stub": {
"content": [
[
[
{
"id": "test"
},
"mock.tests.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
}
]
],
"meta": {
"nf-test": "0.9.0",
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T20:24:23.278625607"
},
"filtered": {
"content": [
[
[
{
"id": "test"
},
"test.filtered.tsv:md5,ecc3ca4c6538f9248dce844108474a66"
]
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T20:24:15.091697173"
},
"versions": {
"content": [
[
"versions.yml:md5,275e382be9ca5bdd30ff5d6fc4340616"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:31:03.847264377"
"timestamp": "2024-12-11T20:24:15.113337441"
}
}
4 changes: 1 addition & 3 deletions modules/nf-core/custom/tabulartogseacls/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,7 @@ process CUSTOM_TABULARTOGSEACLS {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'nf-core/ubuntu:20.04' }"
container "community.wave.seqera.io/library/coreutils:8.30--b947da103164f84b"

input:
tuple val(meta), path(samples)
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6 changes: 4 additions & 2 deletions modules/nf-core/custom/tabulartogseacls/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.cls).match("cls") }
//not asserting versions - bash version differs between conda and container
)
}
}
Expand All @@ -44,7 +45,8 @@ nextflow_process {
then {
assertAll (
{ assert process.success },
{ assert snapshot(process.out).match() },
{ assert snapshot(process.out.cls).match("cls_stub") }
//not asserting versions - bash version differs between conda and container
)
}
}
Expand Down
96 changes: 28 additions & 68 deletions modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,84 +1,44 @@
{
"test_custom_tabulartogseacls - stub": {
"cls_stub": {
"content": [
{
"0": [
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,3374690b043ab72b21680ff1f196841e"
],
"cls": [
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,3374690b043ab72b21680ff1f196841e"
[
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"mock.cls:md5,d41d8cd98f00b204e9800998ecf8427e"
]
}
]
],
"meta": {
"nf-test": "0.9.0",
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:49:29.416602434"
"timestamp": "2024-12-11T20:52:24.849486391"
},
"test_custom_tabulartogseacls": {
"cls": {
"content": [
{
"0": [
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
]
],
"1": [
"versions.yml:md5,3374690b043ab72b21680ff1f196841e"
],
"cls": [
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
]
],
"versions": [
"versions.yml:md5,3374690b043ab72b21680ff1f196841e"
[
[
{
"id": "treatment_mCherry_hND6_sample_number",
"variable": "treatment",
"reference": "mCherry",
"target": "hND6",
"blocking": "sample_number"
},
"treatment_mCherry_hND6_sample_number.cls:md5,7b887159417842b1fe87afebe4f8c2b7"
]
}
]
],
"meta": {
"nf-test": "0.9.0",
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-11T15:49:20.965285853"
"timestamp": "2024-12-11T20:52:12.548858633"
}
}
4 changes: 1 addition & 3 deletions modules/nf-core/custom/tabulartogseagct/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,7 @@ process CUSTOM_TABULARTOGSEAGCT {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'nf-core/ubuntu:20.04' }"
container "community.wave.seqera.io/library/coreutils:8.30--b947da103164f84b"

input:
tuple val(meta), path(tabular)
Expand Down
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