From 34816b7f16036e9682afed3266f6a9a611b6443e Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 15 Jan 2025 11:45:32 -0600 Subject: [PATCH 1/5] Update odgi to version 0.9.0 --- modules/nf-core/odgi/build/environment.yml | 2 +- modules/nf-core/odgi/build/main.nf | 4 ++-- modules/nf-core/odgi/draw/environment.yml | 2 +- modules/nf-core/odgi/draw/main.nf | 4 ++-- modules/nf-core/odgi/layout/environment.yml | 2 +- modules/nf-core/odgi/layout/main.nf | 4 ++-- modules/nf-core/odgi/sort/environment.yml | 2 +- modules/nf-core/odgi/sort/main.nf | 4 ++-- modules/nf-core/odgi/squeeze/environment.yml | 2 +- modules/nf-core/odgi/squeeze/main.nf | 4 ++-- modules/nf-core/odgi/stats/environment.yml | 2 +- modules/nf-core/odgi/stats/main.nf | 4 ++-- modules/nf-core/odgi/unchop/environment.yml | 2 +- modules/nf-core/odgi/unchop/main.nf | 4 ++-- modules/nf-core/odgi/view/environment.yml | 2 +- modules/nf-core/odgi/view/main.nf | 4 ++-- modules/nf-core/odgi/viz/environment.yml | 2 +- modules/nf-core/odgi/viz/main.nf | 4 ++-- 18 files changed, 27 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/odgi/build/environment.yml b/modules/nf-core/odgi/build/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/build/environment.yml +++ b/modules/nf-core/odgi/build/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/build/main.nf b/modules/nf-core/odgi/build/main.nf index c1bf340274b..1604ebc9b12 100644 --- a/modules/nf-core/odgi/build/main.nf +++ b/modules/nf-core/odgi/build/main.nf @@ -4,8 +4,8 @@ process ODGI_BUILD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/draw/environment.yml b/modules/nf-core/odgi/draw/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/draw/environment.yml +++ b/modules/nf-core/odgi/draw/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/draw/main.nf b/modules/nf-core/odgi/draw/main.nf index fa1de741c7e..ebc47201e94 100644 --- a/modules/nf-core/odgi/draw/main.nf +++ b/modules/nf-core/odgi/draw/main.nf @@ -4,8 +4,8 @@ process ODGI_DRAW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph), path(lay) diff --git a/modules/nf-core/odgi/layout/environment.yml b/modules/nf-core/odgi/layout/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/layout/environment.yml +++ b/modules/nf-core/odgi/layout/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/layout/main.nf b/modules/nf-core/odgi/layout/main.nf index 27ae4ae0371..56a789b4a05 100644 --- a/modules/nf-core/odgi/layout/main.nf +++ b/modules/nf-core/odgi/layout/main.nf @@ -4,8 +4,8 @@ process ODGI_LAYOUT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/sort/environment.yml b/modules/nf-core/odgi/sort/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/sort/environment.yml +++ b/modules/nf-core/odgi/sort/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/sort/main.nf b/modules/nf-core/odgi/sort/main.nf index 064624959e1..bbdb5a6e8c4 100644 --- a/modules/nf-core/odgi/sort/main.nf +++ b/modules/nf-core/odgi/sort/main.nf @@ -4,8 +4,8 @@ process ODGI_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/squeeze/environment.yml b/modules/nf-core/odgi/squeeze/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/squeeze/environment.yml +++ b/modules/nf-core/odgi/squeeze/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/squeeze/main.nf b/modules/nf-core/odgi/squeeze/main.nf index 6872fb65d68..9d68edae74c 100644 --- a/modules/nf-core/odgi/squeeze/main.nf +++ b/modules/nf-core/odgi/squeeze/main.nf @@ -4,8 +4,8 @@ process ODGI_SQUEEZE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graphs) diff --git a/modules/nf-core/odgi/stats/environment.yml b/modules/nf-core/odgi/stats/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/stats/environment.yml +++ b/modules/nf-core/odgi/stats/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/stats/main.nf b/modules/nf-core/odgi/stats/main.nf index 48a77415f6e..c963cbc74ba 100644 --- a/modules/nf-core/odgi/stats/main.nf +++ b/modules/nf-core/odgi/stats/main.nf @@ -4,8 +4,8 @@ process ODGI_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/unchop/environment.yml b/modules/nf-core/odgi/unchop/environment.yml index 79e67e2e69c..9e850ef1c78 100644 --- a/modules/nf-core/odgi/unchop/environment.yml +++ b/modules/nf-core/odgi/unchop/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 \ No newline at end of file diff --git a/modules/nf-core/odgi/unchop/main.nf b/modules/nf-core/odgi/unchop/main.nf index 033011c4170..8e74111c21c 100644 --- a/modules/nf-core/odgi/unchop/main.nf +++ b/modules/nf-core/odgi/unchop/main.nf @@ -4,8 +4,8 @@ process ODGI_UNCHOP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/view/environment.yml b/modules/nf-core/odgi/view/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/view/environment.yml +++ b/modules/nf-core/odgi/view/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/view/main.nf b/modules/nf-core/odgi/view/main.nf index 83672e4ed65..6ef7f8a18a0 100644 --- a/modules/nf-core/odgi/view/main.nf +++ b/modules/nf-core/odgi/view/main.nf @@ -4,8 +4,8 @@ process ODGI_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) diff --git a/modules/nf-core/odgi/viz/environment.yml b/modules/nf-core/odgi/viz/environment.yml index 79e67e2e69c..ecfae63b909 100644 --- a/modules/nf-core/odgi/viz/environment.yml +++ b/modules/nf-core/odgi/viz/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::odgi=0.8.4 + - bioconda::odgi=0.9.0 diff --git a/modules/nf-core/odgi/viz/main.nf b/modules/nf-core/odgi/viz/main.nf index 562300eb8d9..a9c21388fca 100644 --- a/modules/nf-core/odgi/viz/main.nf +++ b/modules/nf-core/odgi/viz/main.nf @@ -4,8 +4,8 @@ process ODGI_VIZ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/odgi:0.8.4--py310h6cc9453_0': - 'biocontainers/odgi:0.8.4--py310h6cc9453_0' }" + 'https://depot.galaxyproject.org/singularity/odgi:0.9.0--py312h5e9d817_1': + 'biocontainers/odgi:0.9.0--py312h5e9d817_1' }" input: tuple val(meta), path(graph) From 9c34316fe3b3382eb9a8863536e4c989348ba5eb Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 15 Jan 2025 14:50:46 -0600 Subject: [PATCH 2/5] Update nf-test checksums --- modules/nf-core/odgi/draw/tests/main.nf.test.snap | 14 +++++++++----- modules/nf-core/odgi/sort/tests/main.nf.test.snap | 8 ++++---- .../nf-core/odgi/squeeze/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/odgi/stats/tests/main.nf.test.snap | 8 ++++---- .../nf-core/odgi/unchop/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/odgi/view/tests/main.nf.test.snap | 10 +++++++--- modules/nf-core/odgi/viz/tests/main.nf.test.snap | 10 +++++++--- 7 files changed, 39 insertions(+), 27 deletions(-) diff --git a/modules/nf-core/odgi/draw/tests/main.nf.test.snap b/modules/nf-core/odgi/draw/tests/main.nf.test.snap index f81580f19c2..b0a77f3caf7 100644 --- a/modules/nf-core/odgi/draw/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/draw/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.png:md5,2024bc28ff028163094fa1070da028db" + "test.png:md5,be625ee96d1acd50ba6dbb37102ae6b9" ] ], "1": [ - "versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3" + "versions.yml:md5,227b8d9ac064dec15f0abad54334e4fa" ], "png": [ [ @@ -20,14 +20,18 @@ "id": "test", "single_end": false }, - "test.png:md5,2024bc28ff028163094fa1070da028db" + "test.png:md5,be625ee96d1acd50ba6dbb37102ae6b9" ] ], "versions": [ - "versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3" + "versions.yml:md5,227b8d9ac064dec15f0abad54334e4fa" ] } ], - "timestamp": "2024-01-30T11:03:39.412763234" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-15T14:46:28.331207" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/sort/tests/main.nf.test.snap b/modules/nf-core/odgi/sort/tests/main.nf.test.snap index 6f82698261d..4a4e0b8cb69 100644 --- a/modules/nf-core/odgi/sort/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/sort/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "test.og", [ - "versions.yml:md5,6defcba99b79fde2042de15eec929bf4" + "versions.yml:md5,642e4ce5c2288d3b6e4f231396ecd5b4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-08-13T09:40:56.821872" + "timestamp": "2025-01-15T14:47:49.015053" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap b/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap index 0aa99cb9a66..0a75df87b80 100644 --- a/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/squeeze/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "test.og", [ - "versions.yml:md5,ee7ed77636f98e98a3e40a915c22ed64" + "versions.yml:md5,751fb4a0629a070f0edc989c4d5e555b" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-08-13T10:09:07.409463" + "timestamp": "2025-01-15T14:48:22.366465" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/stats/tests/main.nf.test.snap b/modules/nf-core/odgi/stats/tests/main.nf.test.snap index a36be4ef95e..269ecd3f2c6 100644 --- a/modules/nf-core/odgi/stats/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/stats/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "test.og.stats.tsv", [ - "versions.yml:md5,0f4d685d1c0d3562081073bfbf85d95d" + "versions.yml:md5,5127b79951be7dcc7925348293826aea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-08-09T09:55:15.438306" + "timestamp": "2025-01-15T14:48:52.45995" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/unchop/tests/main.nf.test.snap b/modules/nf-core/odgi/unchop/tests/main.nf.test.snap index f4744bd4b89..9d62a62fa44 100644 --- a/modules/nf-core/odgi/unchop/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/unchop/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "test.og", [ - "versions.yml:md5,721a9406e96a94ccb0ec44dc4f76ed09" + "versions.yml:md5,23b7ff2375170fe1ed6a50e018fbefb1" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.3" }, - "timestamp": "2024-08-13T09:38:53.743369" + "timestamp": "2025-01-15T14:49:21.848525" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/view/tests/main.nf.test.snap b/modules/nf-core/odgi/view/tests/main.nf.test.snap index 1d9fc9671fb..1379b97641d 100644 --- a/modules/nf-core/odgi/view/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/view/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,cda909193ec196138daed6da151a8e83" + "versions.yml:md5,6839cfd47e1e750fee7a947807dce2a7" ], "gfa": [ [ @@ -24,10 +24,14 @@ ] ], "versions": [ - "versions.yml:md5,cda909193ec196138daed6da151a8e83" + "versions.yml:md5,6839cfd47e1e750fee7a947807dce2a7" ] } ], - "timestamp": "2024-01-30T10:35:28.605315319" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-15T14:49:51.203182" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/viz/tests/main.nf.test.snap b/modules/nf-core/odgi/viz/tests/main.nf.test.snap index 49e909ba966..62d386e1f1c 100644 --- a/modules/nf-core/odgi/viz/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/viz/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,95c0ee8015cf342c2724fb64d4cba67e" + "versions.yml:md5,d819e8f806b414b178c2d915e9d9791e" ], "png": [ [ @@ -24,10 +24,14 @@ ] ], "versions": [ - "versions.yml:md5,95c0ee8015cf342c2724fb64d4cba67e" + "versions.yml:md5,d819e8f806b414b178c2d915e9d9791e" ] } ], - "timestamp": "2024-01-30T09:53:51.373368285" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-15T14:50:21.102589" } } \ No newline at end of file From d722598a65c0a0c62b9651faebf9c79f481c7ed5 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 17 Jan 2025 10:51:26 -0600 Subject: [PATCH 3/5] Assert output file(s) exist --- modules/nf-core/odgi/build/tests/main.nf.test | 4 +--- modules/nf-core/odgi/layout/tests/main.nf.test | 6 +++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/odgi/build/tests/main.nf.test b/modules/nf-core/odgi/build/tests/main.nf.test index d2f6a5f5813..eee49902fb3 100644 --- a/modules/nf-core/odgi/build/tests/main.nf.test +++ b/modules/nf-core/odgi/build/tests/main.nf.test @@ -25,10 +25,8 @@ nextflow_process { then { assertAll( { assert process.success }, -// { assert snapshot(process.out).match() } // the odgi file on disk may not be deterministic, but the graph itself is + { assert path(process.out.og.get(0).get(1)).exists() } // the odgi file on disk may not be deterministic, but the graph itself is ) } - } - } diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test b/modules/nf-core/odgi/layout/tests/main.nf.test index f8daf7034c0..e98222cdc7c 100644 --- a/modules/nf-core/odgi/layout/tests/main.nf.test +++ b/modules/nf-core/odgi/layout/tests/main.nf.test @@ -26,10 +26,10 @@ nextflow_process { then { assertAll( { assert process.success }, -// { assert snapshot(process.out).match() } // odgi layout is not deterministic + // odgi layout is not deterministic + { assert path(process.out.lay.get(0).get(1)).exists() }, + { assert path(process.out.tsv.get(0).get(1)).exists() } ) } - } - } From 58c7b356a4122faf5bdc562b447bb1396df73560 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 22 Jan 2025 10:19:41 -0800 Subject: [PATCH 4/5] Assert versions match --- modules/nf-core/odgi/build/tests/main.nf.test | 1 + modules/nf-core/odgi/draw/tests/main.nf.test | 2 -- modules/nf-core/odgi/layout/tests/main.nf.test | 1 + 3 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/odgi/build/tests/main.nf.test b/modules/nf-core/odgi/build/tests/main.nf.test index eee49902fb3..033e37ae861 100644 --- a/modules/nf-core/odgi/build/tests/main.nf.test +++ b/modules/nf-core/odgi/build/tests/main.nf.test @@ -25,6 +25,7 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert snapshot(process.out.versions).match()}, { assert path(process.out.og.get(0).get(1)).exists() } // the odgi file on disk may not be deterministic, but the graph itself is ) } diff --git a/modules/nf-core/odgi/draw/tests/main.nf.test b/modules/nf-core/odgi/draw/tests/main.nf.test index 8b59a7f80ab..a783ba3461f 100644 --- a/modules/nf-core/odgi/draw/tests/main.nf.test +++ b/modules/nf-core/odgi/draw/tests/main.nf.test @@ -29,7 +29,5 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - } diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test b/modules/nf-core/odgi/layout/tests/main.nf.test index e98222cdc7c..3d64c84526a 100644 --- a/modules/nf-core/odgi/layout/tests/main.nf.test +++ b/modules/nf-core/odgi/layout/tests/main.nf.test @@ -26,6 +26,7 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert snapshot(process.out.versions).match()}, // odgi layout is not deterministic { assert path(process.out.lay.get(0).get(1)).exists() }, { assert path(process.out.tsv.get(0).get(1)).exists() } From 71f1f8ace1b13ed372166e238b00c1883859d838 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Wed, 22 Jan 2025 10:31:58 -0800 Subject: [PATCH 5/5] Update test snapshots --- .../odgi/build/tests/main.nf.test.snap | 35 +++--------- .../odgi/layout/tests/main.nf.test.snap | 53 +++---------------- 2 files changed, 16 insertions(+), 72 deletions(-) diff --git a/modules/nf-core/odgi/build/tests/main.nf.test.snap b/modules/nf-core/odgi/build/tests/main.nf.test.snap index f2254ad00fb..8f79fa080f5 100644 --- a/modules/nf-core/odgi/build/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/build/tests/main.nf.test.snap @@ -1,33 +1,14 @@ { "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.og:md5,8660c0f724a54d7346575ac38ff0b329" - ] - ], - "1": [ - "versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553" - ], - "og": [ - [ - { - "id": "test", - "single_end": false - }, - "test.og:md5,8660c0f724a54d7346575ac38ff0b329" - ] - ], - "versions": [ - "versions.yml:md5,57e730c18f2ab7d51bd8ca113e39d553" - ] - } + [ + "versions.yml:md5,ac55cdc779839b4b8de83f0a757c8671" + ] ], - "timestamp": "2024-01-30T11:07:44.462811986" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-22T10:31:31.313418" } } \ No newline at end of file diff --git a/modules/nf-core/odgi/layout/tests/main.nf.test.snap b/modules/nf-core/odgi/layout/tests/main.nf.test.snap index df8dcf35c21..d065384f064 100644 --- a/modules/nf-core/odgi/layout/tests/main.nf.test.snap +++ b/modules/nf-core/odgi/layout/tests/main.nf.test.snap @@ -1,51 +1,14 @@ { "homo_sapiens - pangenome - pangenome_smoothxg_gfa": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test.lay:md5,ce4ee2f434717077f5c765a5a82fd978" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,7bf353889ac6dfcce8b38618d760f144" - ] - ], - "2": [ - "versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b" - ], - "lay": [ - [ - { - "id": "test", - "single_end": false - }, - "test.lay:md5,ce4ee2f434717077f5c765a5a82fd978" - ] - ], - "tsv": [ - [ - { - "id": "test", - "single_end": false - }, - "test.tsv:md5,7bf353889ac6dfcce8b38618d760f144" - ] - ], - "versions": [ - "versions.yml:md5,c0207add403de5e7011f368a4cfd3b2b" - ] - } + [ + "versions.yml:md5,ee823dcfb065a7234f0c4e2241651939" + ] ], - "timestamp": "2024-01-30T10:58:20.958731752" + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.3" + }, + "timestamp": "2025-01-22T10:31:46.13426" } } \ No newline at end of file