Merge pull request #793 from d4straub/update-modules-2.12.0dev

Update Picrust2 and nf-core modules
nf-core · Nov 12, 2024 · 9cb08c2 · 9cb08c2
2 parents 65bada8 + 2c22f74
commit 9cb08c2
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Showing 23 changed files with 671 additions and 232 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,17 +15,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#792](https://github.com/nf-core/ampliseq/pull/792) - Remove white spaces in process tags to avoid errors on some systems
 - [#785](https://github.com/nf-core/ampliseq/pull/785) - Template update for nf-core/tools version 3.0.2
 - [#786](https://github.com/nf-core/ampliseq/pull/786) - Creation of the summary report was failing with `--dada_ref_taxonomy silva=132`
+- [#792](https://github.com/nf-core/ampliseq/pull/792) - Remove white spaces in process tags to avoid errors on some systems
 
 ### `Dependencies`
 
 - [#785](https://github.com/nf-core/ampliseq/pull/785) - Update MultiQC
+- [#793](https://github.com/nf-core/ampliseq/pull/793) - Update Picrust2 and nf-core modules
 
 | software | previously | now    |
 | -------- | ---------- | ------ |
 | MultiQC  | 1.21       | 1.25.1 |
+| Picrust2 | 2.5.2      | 2.5.3  |
 
 ### `Removed`
 

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "cutadapt": {
                         "branch": "master",
-                        "git_sha": "6618151ed69274863dc6fe6d2920afa90abaca1f",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "epang/place": {
@@ -62,7 +62,7 @@
                     },
                     "kraken2/kraken2": {
                         "branch": "master",
-                        "git_sha": "653218e79ffa76fde20319e9062f8b8da5cf7555",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
                     },
@@ -89,17 +89,17 @@
                     },
                     "vsearch/cluster": {
                         "branch": "master",
-                        "git_sha": "d97b335eb448073c1b680710303c02a55f40c77c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "vsearch/sintax": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "vsearch/usearchglobal": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/picrust.nf b/modules/local/picrust.nf
@@ -2,10 +2,10 @@ process PICRUST {
     tag "${seq},${abund}"
     label 'process_medium'
 
-    conda "bioconda::picrust2=2.5.2"
+    conda "bioconda::picrust2=2.5.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/picrust2:2.5.2--pyhdfd78af_0' :
-        'biocontainers/picrust2:2.5.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/picrust2:2.5.3--pyhdfd78af_0' :
+        'biocontainers/picrust2:2.5.3--pyhdfd78af_0' }"
 
     input:
     path(seq)

diff --git a/modules/nf-core/cutadapt/environment.yml b/modules/nf-core/cutadapt/environment.yml
diff --git a/modules/nf-core/cutadapt/meta.yml b/modules/nf-core/cutadapt/meta.yml
diff --git a/modules/nf-core/cutadapt/tests/main.nf.test b/modules/nf-core/cutadapt/tests/main.nf.test
diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml
diff --git a/modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff b/modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff
diff --git a/modules/nf-core/kraken2/kraken2/main.nf b/modules/nf-core/kraken2/kraken2/main.nf
diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml
diff --git a/modules/nf-core/kraken2/kraken2/tests/main.nf.test b/modules/nf-core/kraken2/kraken2/tests/main.nf.test