Update seqkit to version 2.9.0 (#7315)

* Update seqkit to version 2.9.0 * Add stub sections where missing * Update nf-test checksums * Use valid gzip files in stub * Update nf-test checksums for subworkflows * Update versions checksums manually
nf-core · Jan 17, 2025 · 60645c2 · 60645c2
1 parent e78f286
commit 60645c2
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Showing 40 changed files with 397 additions and 400 deletions.
diff --git a/modules/nf-core/seqkit/concat/environment.yml b/modules/nf-core/seqkit/concat/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::seqkit=2.8.1"
+  - "bioconda::seqkit=2.9.0"
diff --git a/modules/nf-core/seqkit/concat/main.nf b/modules/nf-core/seqkit/concat/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_CONCAT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(input, stageAs: 'in/*')

diff --git a/modules/nf-core/seqkit/concat/tests/main.nf.test.snap b/modules/nf-core/seqkit/concat/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "sarscov2 and human primers - fasta": {
         "content": [
             [
-                "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:33:12.38186745"
+        "timestamp": "2025-01-15T15:06:45.246143"
     },
     "sarscov2 and human primers - fasta - stub": {
         "content": [
@@ -23,7 +23,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                    "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
                 ],
                 "fastx": [
                     [
@@ -34,14 +34,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,32d898698c9224f989b9527fe0b948d4"
+                    "versions.yml:md5,13b312c8ca94f9c6460ffc759a5c79c9"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T08:33:22.533226274"
+        "timestamp": "2025-01-15T15:06:49.428563"
     }
 }
diff --git a/modules/nf-core/seqkit/fq2fa/environment.yml b/modules/nf-core/seqkit/fq2fa/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/fq2fa/main.nf b/modules/nf-core/seqkit/fq2fa/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_FQ2FA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0' :
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0' :
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastq)

diff --git a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ],
                 "fasta": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-13T08:56:21.234724552"
+        "timestamp": "2025-01-15T15:07:44.366504"
     },
     "sarscov2 - bam": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ],
                 "fasta": [
                     [
@@ -59,14 +59,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,70efc6839fd6443ee9116c082a730f72"
+                    "versions.yml:md5,9799aeba106e1fd61b65fd876eabd863"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-13T08:55:54.648865102"
+        "timestamp": "2025-01-15T15:07:40.187352"
     }
 }
diff --git a/modules/nf-core/seqkit/grep/environment.yml b/modules/nf-core/seqkit/grep/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/grep/main.nf b/modules/nf-core/seqkit/grep/main.nf
@@ -5,8 +5,8 @@ process SEQKIT_GREP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(sequence)

diff --git a/modules/nf-core/seqkit/grep/tests/main.nf.test.snap b/modules/nf-core/seqkit/grep/tests/main.nf.test.snap
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -24,15 +24,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:33:47.542049206"
+        "timestamp": "2025-01-15T15:08:46.340613"
     },
     "with_pattern": {
         "content": [
@@ -47,7 +47,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:38:28.77443193"
+        "timestamp": "2025-01-15T15:08:55.077598"
     },
     "with_file - stub": {
         "content": [
@@ -82,7 +82,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ],
                 "filter": [
                     [
@@ -94,14 +94,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2b6d2bf7e727f835a915128c179cebfa"
+                    "versions.yml:md5,a89075d71a71766480983dc451a119d2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:34:12.85678016"
+        "timestamp": "2025-01-15T15:09:03.009991"
     }
 }
diff --git a/modules/nf-core/seqkit/pair/environment.yml b/modules/nf-core/seqkit/pair/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/pair/main.nf b/modules/nf-core/seqkit/pair/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_PAIR {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)

diff --git a/modules/nf-core/seqkit/pair/tests/main.nf.test.snap b/modules/nf-core/seqkit/pair/tests/main.nf.test.snap
@@ -18,7 +18,7 @@
 
                 ],
                 "2": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ],
                 "reads": [
                     [
@@ -36,15 +36,15 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-08T10:11:09.767703292"
+        "timestamp": "2025-01-15T15:09:51.247775"
     },
     "sarscov2 - bam": {
         "content": [
@@ -65,7 +65,7 @@
 
                 ],
                 "2": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ],
                 "reads": [
                     [
@@ -83,14 +83,14 @@
 
                 ],
                 "versions": [
-                    "versions.yml:md5,77fbea93a3c50ec0f6da886d9849622e"
+                    "versions.yml:md5,8281825c657e9ddabacfeb0d1c07f11e"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.3"
         },
-        "timestamp": "2024-05-07T15:54:57.649454879"
+        "timestamp": "2025-01-15T15:09:46.914754"
     }
 }
diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml
@@ -2,4 +2,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::seqkit=2.8.1
+  - bioconda::seqkit=2.9.0
diff --git a/modules/nf-core/seqkit/replace/main.nf b/modules/nf-core/seqkit/replace/main.nf
@@ -4,8 +4,8 @@ process SEQKIT_REPLACE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/seqkit:2.8.1--h9ee0642_0':
-        'biocontainers/seqkit:2.8.1--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/seqkit:2.9.0--h9ee0642_0':
+        'biocontainers/seqkit:2.9.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(fastx)