Update odgi to version 0.9.0 (#7313)

* Update odgi to version 0.9.0 * Update nf-test checksums * Assert output file(s) exist * Assert versions match * Update test snapshots --------- Co-authored-by: Simon Heumos <simon.heumos@qbic.uni-tuebingen.de>
nf-core · Jan 23, 2025 · 759d9b3 · 759d9b3
1 parent c898ced
commit 759d9b3
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Showing 30 changed files with 88 additions and 134 deletions.
diff --git 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
@@ -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/build/tests/main.nf.test b/modules/nf-core/odgi/build/tests/main.nf.test
@@ -25,10 +25,9 @@ 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 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/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"
     }
 }
diff --git 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
@@ -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/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/draw/tests/main.nf.test.snap b/modules/nf-core/odgi/draw/tests/main.nf.test.snap
@@ -8,26 +8,30 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.png:md5,2024bc28ff028163094fa1070da028db"
+                        "test.png:md5,be625ee96d1acd50ba6dbb37102ae6b9"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,d1ce3da3324df7e6c4531385ad24dbb3"
+                    "versions.yml:md5,227b8d9ac064dec15f0abad54334e4fa"
                 ],
                 "png": [
                     [
                         {
                             "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"
     }
 }
diff --git 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
@@ -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/layout/tests/main.nf.test b/modules/nf-core/odgi/layout/tests/main.nf.test
@@ -26,10 +26,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-//                { assert snapshot(process.out).match() } // odgi layout is not deterministic
+                { 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() }
             )
         }
-
     }
-
 }
diff --git 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"
     }
 }
diff --git 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
@@ -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/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"
     }
 }
diff --git 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
@@ -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/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"
     }
 }
diff --git 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
@@ -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/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"
     }
 }
diff --git 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
diff --git 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/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"
     }
 }
diff --git 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
@@ -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)
-Original file line number
+Diff line change
@@ Expand Up / @@ -29,7 +29,5 @@ nextflow_process { @@
                     { assert snapshot(process.out).match() }
                 )
             }
         }
     }