From e54ce38e5713720b6f0aa76bd1ea6dcb84630ef1 Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Wed, 11 Dec 2024 20:55:52 +0000 Subject: [PATCH] Fix conda tests --- .../custom/matrixfilter/tests/main.nf.test | 8 +- .../matrixfilter/tests/main.nf.test.snap | 192 +++++++----------- .../nf-core/custom/tabulartogseacls/main.nf | 4 +- .../tabulartogseacls/tests/main.nf.test | 6 +- .../tabulartogseacls/tests/main.nf.test.snap | 96 +++------ .../nf-core/custom/tabulartogseagct/main.nf | 4 +- .../tabulartogseagct/tests/main.nf.test | 4 +- .../tabulartogseagct/tests/main.nf.test.snap | 96 +++------ 8 files changed, 147 insertions(+), 263 deletions(-) diff --git a/modules/nf-core/custom/matrixfilter/tests/main.nf.test b/modules/nf-core/custom/matrixfilter/tests/main.nf.test index fc4c8ad69bb..c574fc2927d 100644 --- a/modules/nf-core/custom/matrixfilter/tests/main.nf.test +++ b/modules/nf-core/custom/matrixfilter/tests/main.nf.test @@ -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") } ) } } @@ -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") } ) } } diff --git a/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap b/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap index b34f0f622b8..520efac0ca7 100644 --- a/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap +++ b/modules/nf-core/custom/matrixfilter/tests/main.nf.test.snap @@ -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" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tabulartogseacls/main.nf b/modules/nf-core/custom/tabulartogseacls/main.nf index 23cc3f4d973..43dcd2367ee 100644 --- a/modules/nf-core/custom/tabulartogseacls/main.nf +++ b/modules/nf-core/custom/tabulartogseacls/main.nf @@ -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) diff --git a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test index c31288b174b..894bae6d8c5 100644 --- a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test +++ b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test @@ -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 ) } } @@ -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 ) } } diff --git a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap index 55d8c5a5755..5379ef2f857 100644 --- a/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tabulartogseacls/tests/main.nf.test.snap @@ -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" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tabulartogseagct/main.nf b/modules/nf-core/custom/tabulartogseagct/main.nf index 768305b271d..5a4b30f0fd2 100644 --- a/modules/nf-core/custom/tabulartogseagct/main.nf +++ b/modules/nf-core/custom/tabulartogseagct/main.nf @@ -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) diff --git a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test index 2c3cd77552b..a7def1fe75b 100644 --- a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test +++ b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test @@ -23,7 +23,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.gct).match("gct") } ) } } @@ -43,7 +43,7 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out).match() }, + { assert snapshot(process.out.gct).match("gct_stub") } ) } } diff --git a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap index bbf73b8f883..b6c67f0074c 100644 --- a/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tabulartogseagct/tests/main.nf.test.snap @@ -1,84 +1,44 @@ { - "test_custom_tabulartogseagct": { + "gct_stub": { "content": [ - { - "0": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee" - ] - ], - "1": [ - "versions.yml:md5,de91ab15d8517772e8dc9e8c12c8b552" - ], - "gct": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee" - ] - ], - "versions": [ - "versions.yml:md5,de91ab15d8517772e8dc9e8c12c8b552" + [ + [ + { + "id": "treatment_mCherry_hND6_", + "variable": "treatment", + "reference": "mCherry", + "target": "hND6", + "blocking": "" + }, + "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e" ] - } + ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-11T17:35:50.398934861" + "timestamp": "2024-12-11T20:55:04.058475275" }, - "test_custom_tabulartogseagct - stub": { + "gct": { "content": [ - { - "0": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ - "versions.yml:md5,de91ab15d8517772e8dc9e8c12c8b552" - ], - "gct": [ - [ - { - "id": "treatment_mCherry_hND6_", - "variable": "treatment", - "reference": "mCherry", - "target": "hND6", - "blocking": "" - }, - "mock.gct:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "versions": [ - "versions.yml:md5,de91ab15d8517772e8dc9e8c12c8b552" + [ + [ + { + "id": "treatment_mCherry_hND6_", + "variable": "treatment", + "reference": "mCherry", + "target": "hND6", + "blocking": "" + }, + "treatment_mCherry_hND6_.gct:md5,9727aca45da7ebe619a1f964c9813eee" ] - } + ] ], "meta": { - "nf-test": "0.9.0", + "nf-test": "0.9.2", "nextflow": "24.10.2" }, - "timestamp": "2024-12-11T17:35:58.084545848" + "timestamp": "2024-12-11T20:54:51.98922569" } } \ No newline at end of file