Updates to differentialabundance modules

nf-core · Feb 13, 2025 · a64289e · a64289e
1 parent 9de6d9e
commit a64289e
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Showing 5 changed files with 6 additions and 18 deletions.
diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml
@@ -5,8 +5,3 @@ channels:
   - bioconda
 dependencies:
   - conda-forge::coreutils=9.5
-  - conda-forge::grep=3.11
-  - conda-forge::gzip=1.13
-  - conda-forge::lbzip2=2.5
-  - conda-forge::sed=4.8
-  - conda-forge::tar=1.34
diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml
@@ -5,8 +5,3 @@ channels:
   - bioconda
 dependencies:
   - conda-forge::coreutils=9.5
-  - conda-forge::grep=3.11
-  - conda-forge::gzip=1.13
-  - conda-forge::lbzip2=2.5
-  - conda-forge::sed=4.8
-  - conda-forge::tar=1.34
diff --git a/modules/nf-core/gprofiler2/gost/main.nf b/modules/nf-core/gprofiler2/gost/main.nf
@@ -43,7 +43,6 @@ process GPROFILER2_GOST {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
         r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
         r-gprofiler2: \$(Rscript -e "library(gprofiler2); cat(as.character(packageVersion('gprofiler2')))")
     END_VERSIONS

diff --git a/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R b/modules/nf-core/gprofiler2/gost/templates/gprofiler2_gost.R
@@ -453,7 +453,6 @@ ggplot2.version <- as.character(packageVersion('ggplot2'))
 writeLines(
     c(
         '"$task.process":',
-        paste('    r-base:', r.version),
         paste('    r-ggplot2:', ggplot2.version),
         paste('    r-gprofiler2:', gprofiler2.version)
     ),

diff --git a/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap b/modules/nf-core/gprofiler2/gost/tests/main.nf.test.snap
@@ -54,7 +54,7 @@
                 "R_sessionInfo.log"
             ],
             [
-                "versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069"
+                "versions.yml:md5,1126f61c24d10b3d9e767aa0240b6178"
             ],
             [
                 "Condition_genotype_WT_KO.gprofiler2.gostplot.html"
@@ -67,7 +67,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.4"
         },
-        "timestamp": "2025-02-07T15:34:05.718473191"
+        "timestamp": "2025-02-13T15:30:11.459755332"
     },
     "stub": {
         "content": [
@@ -169,7 +169,7 @@
                     ]
                 ],
                 "8": [
-                    "versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069"
+                    "versions.yml:md5,1126f61c24d10b3d9e767aa0240b6178"
                 ],
                 "all_enrich": [
                     [
@@ -268,14 +268,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,7ff4ab78463faf97bba7e698ed9a9069"
+                    "versions.yml:md5,1126f61c24d10b3d9e767aa0240b6178"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2025-01-21T11:31:33.394855046"
+        "timestamp": "2025-02-13T15:30:19.733789446"
     }
 }