Update to LAST version 1608 using sequera containers.

This version will be needed for the use of the new maf-linked tool later.
nf-core · Jan 22, 2025 · faf5a37 · faf5a37
1 parent e7f7c0f
commit faf5a37
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Showing 25 changed files with 101 additions and 101 deletions.
diff --git a/modules/nf-core/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml
@@ -3,4 +3,4 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::last=1595
+  - bioconda::last=1608
diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf
@@ -3,9 +3,9 @@ process LAST_DOTPLOT {
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' :
-        'biocontainers/last:1595--h43eeafb_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
+        : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
 
     input:
     tuple val(meta), path(maf), path(annot_b)

diff --git a/modules/nf-core/last/dotplot/tests/main.nf.test.snap b/modules/nf-core/last/dotplot/tests/main.nf.test.snap
@@ -2,37 +2,37 @@
     "sarscov2 - contigs - genome - gif": {
         "content": [
             [
-                "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f"
+                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:22:21.508978"
+        "timestamp": "2025-01-21T09:18:32.629314"
     },
     "sarscov2 - contigs - genome - png - stub": {
         "content": [
             [
-                "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f"
+                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:22:37.504391"
+        "timestamp": "2025-01-21T09:18:48.084683"
     },
     "sarscov2 - contigs - genome - png": {
         "content": [
             [
-                "versions.yml:md5,4faa6f4aecf50e689d84709648818a9f"
+                "versions.yml:md5,143ef48514afd0c39da64d8f11fd18f7"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:22:05.800777"
+        "timestamp": "2025-01-21T09:18:17.971205"
     }
 }
diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml
@@ -3,4 +3,4 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::last=1595
+  - bioconda::last=1608
diff --git a/modules/nf-core/last/lastal/main.nf b/modules/nf-core/last/lastal/main.nf
@@ -3,9 +3,9 @@ process LAST_LASTAL {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' :
-        'biocontainers/last:1595--h43eeafb_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
+        : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
 
     input:
     tuple val(meta), path(fastx), path (param_file)

diff --git a/modules/nf-core/last/lastal/tests/main.nf.test.snap b/modules/nf-core/last/lastal/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.maf.gz:md5,fac3fd9e98f2fac019e09d434634e542"
+                        "contigs.maf.gz:md5,3729bf099fecb196b8b5b49fc3487b56"
                     ]
                 ],
                 "1": [
@@ -17,19 +17,19 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74"
+                        "contigs.tsv:md5,38d678f139ea70765ce29966c743487b"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ],
                 "maf": [
                     [
                         {
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.maf.gz:md5,fac3fd9e98f2fac019e09d434634e542"
+                        "contigs.maf.gz:md5,3729bf099fecb196b8b5b49fc3487b56"
                     ]
                 ],
                 "multiqc": [
@@ -38,19 +38,19 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.tsv:md5,f028e69bd64e54080b9a03fd809cba74"
+                        "contigs.tsv:md5,38d678f139ea70765ce29966c743487b"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:27:20.528278"
+        "timestamp": "2025-01-22T10:13:12.144354"
     },
     "sarscov2 - contigs - genome - stub": {
         "content": [
@@ -74,7 +74,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ],
                 "maf": [
                     [
@@ -95,15 +95,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:28:03.933791"
+        "timestamp": "2025-01-22T10:15:14.385573"
     },
     "sarscov2 - contigs - genome - withparams": {
         "content": [
@@ -114,7 +114,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.maf.gz:md5,5c4e2c43ed5371453a88a72586577f39"
+                        "contigs.maf.gz:md5,b2ea256c960899555dbc3fd1acbc43b4"
                     ]
                 ],
                 "1": [
@@ -127,15 +127,15 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ],
                 "maf": [
                     [
                         {
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.maf.gz:md5,5c4e2c43ed5371453a88a72586577f39"
+                        "contigs.maf.gz:md5,b2ea256c960899555dbc3fd1acbc43b4"
                     ]
                 ],
                 "multiqc": [
@@ -148,14 +148,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,defd389a6cc838d0cc9c6ec1dcea81c5"
+                    "versions.yml:md5,23bb5d428e31caed85e991482fa9f967"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:27:42.180309"
+        "timestamp": "2025-01-22T10:14:13.280646"
     }
 }
diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml
@@ -3,4 +3,4 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::last=1595
+  - bioconda::last=1608
diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf
@@ -3,9 +3,9 @@ process LAST_LASTDB {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' :
-        'biocontainers/last:1595--h43eeafb_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
+        : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
 
     input:
     tuple val(meta), path(fastx)

diff --git a/modules/nf-core/last/lastdb/tests/main.nf.test.snap b/modules/nf-core/last/lastdb/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ],
                 "index": [
                     [
@@ -38,15 +38,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:28:57.035523"
+        "timestamp": "2025-01-22T10:16:49.233187"
     },
     "sarscov2 - fastq gzipped": {
         "content": [
@@ -59,7 +59,7 @@
                         [
                             "test.bck:md5,05b14d8ac418b3193d9cc921086cea05",
                             "test.des:md5,26ab49015cc572172b9efa50fc5190bc",
-                            "test.prj:md5,94d4c9b51136494870775837d7e7f06c",
+                            "test.prj:md5,a9e1fa5d50afd39e57aaab489ca2b0a2",
                             "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b",
                             "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da",
                             "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0",
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ],
                 "index": [
                     [
@@ -78,7 +78,7 @@
                         [
                             "test.bck:md5,05b14d8ac418b3193d9cc921086cea05",
                             "test.des:md5,26ab49015cc572172b9efa50fc5190bc",
-                            "test.prj:md5,94d4c9b51136494870775837d7e7f06c",
+                            "test.prj:md5,a9e1fa5d50afd39e57aaab489ca2b0a2",
                             "test.sds:md5,d3deb4c985081c9f5ad6684d405bd20b",
                             "test.ssp:md5,5c17139a9022b0cb97f007146fa1c6da",
                             "test.suf:md5,9ac359afa86a8964d81a87a1d4f05ef0",
@@ -87,15 +87,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:28:40.861818"
+        "timestamp": "2025-01-22T10:16:13.506203"
     },
     "sarscov2 - fasta": {
         "content": [
@@ -108,7 +108,7 @@
                         [
                             "test.bck:md5,157526d333b88523cb15ac4efe00738f",
                             "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc",
-                            "test.prj:md5,73136d767ab23467bd6fd80b85376369",
+                            "test.prj:md5,10b52b9f5adad3b9afd3d73897e588f9",
                             "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015",
                             "test.ssp:md5,53524efdea3d8989201419a29e81ec1f",
                             "test.suf:md5,ef7482260705bb8146acbbbdce6c0068",
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ],
                 "index": [
                     [
@@ -127,7 +127,7 @@
                         [
                             "test.bck:md5,157526d333b88523cb15ac4efe00738f",
                             "test.des:md5,3a9ea6d336e113a74d7fdca5e7b623fc",
-                            "test.prj:md5,73136d767ab23467bd6fd80b85376369",
+                            "test.prj:md5,10b52b9f5adad3b9afd3d73897e588f9",
                             "test.sds:md5,e7729db27ac7a5a109c9d48cfcdc9015",
                             "test.ssp:md5,53524efdea3d8989201419a29e81ec1f",
                             "test.suf:md5,ef7482260705bb8146acbbbdce6c0068",
@@ -136,14 +136,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9b9adf5e1036575622de89a2183d60f1"
+                    "versions.yml:md5,8b5e6ad969c610f963ab9ec6bddea60e"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.10.3"
         },
-        "timestamp": "2024-12-17T18:28:25.358778"
+        "timestamp": "2025-01-22T10:15:48.482722"
     }
 }
diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml
@@ -3,4 +3,4 @@ channels:
   - bioconda
 
 dependencies:
-  - bioconda::last=1595
+  - bioconda::last=1608
diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf
@@ -3,9 +3,9 @@ process LAST_MAFCONVERT {
     label 'process_high'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/last:1595--h43eeafb_0' :
-        'biocontainers/last:1595--h43eeafb_0' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
+        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/db/db0b5de918238f07ec1ca668be942397da85e26aa582f8927ac37c70896303cf/data'
+        : 'community.wave.seqera.io/library/last:1608--f41c047f7dc37e30'}"
 
     input:
     tuple val(meta), path(maf)