Merge branch 'dev' into docs-review

PGScatalog · Jul 30, 2024 · c5d0679 · c5d0679
2 parents 3453918 + f9c4624
commit c5d0679
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Showing 9 changed files with 20 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -43,7 +43,7 @@ process {
     }
 
     withLabel: plink2 {
-        ext.conda = "bioconda::plink2==2.00a5.10"
+        ext.conda = "$projectDir/environments/plink2/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/plink2'
         ext.singularity = 'oras://ghcr.io/pgscatalog/plink2'
         ext.docker_version = ':2.00a5.10'
@@ -67,7 +67,7 @@ process {
     }
 
     withLabel: pyyaml {
-        ext.conda = "conda-forge::pyyaml==6.0"
+        ext.conda = "$projectDir/environments/pyyaml/environment.yml"
         ext.singularity = 'oras://ghcr.io/pgscatalog/pyyaml'
         ext.singularity_version = ':6.0-singularity'
         ext.docker = 'ghcr.io/pgscatalog/pyyaml'

diff --git a/environments/fraposa/environment.yml b/environments/fraposa/environment.yml
@@ -2,5 +2,6 @@ name: fraposa-pgsc
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- fraposa-pgsc=1.0.0
+  - fraposa-pgsc=1.0.0
diff --git a/environments/pgscatalog_utils/environment.yml b/environments/pgscatalog_utils/environment.yml
@@ -2,5 +2,6 @@ name: pgscatalog-utils
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- pgscatalog-utils=1.2.0
+  - pgscatalog-utils=1.2.0
diff --git a/environments/plink2/environment.yml b/environments/plink2/environment.yml
@@ -0,0 +1,7 @@
+name: plink2
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults  
+dependencies: 
+  - plink2==2.00a5.10
diff --git a/environments/pyyaml/environment.yml b/environments/pyyaml/environment.yml
@@ -2,6 +2,6 @@ name: pyyaml
 channels:
   - conda-forge
   - bioconda
-  - defaults
+  - nodefaults
 dependencies:
-- pyyaml=6.0.1
+  - pyyaml=6.0.1
diff --git a/environments/report/environment.yml b/environments/report/environment.yml
@@ -2,6 +2,7 @@ name: report
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies: 
   - r-jsonlite
   - r-dplyr

diff --git a/environments/zstd/environment.yml b/environments/zstd/environment.yml
@@ -2,5 +2,6 @@ name: zstd
 channels:
   - conda-forge
   - bioconda
+  - nodefaults  
 dependencies:
-- zstd=1.4.8
+  - zstd=1.4.8
diff --git a/nextflow.config b/nextflow.config
@@ -258,7 +258,7 @@ manifest {
     description     = 'The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.10.0'
-    version         = '2.0.0-beta.1'
+    version         = '2.0.0-beta.2'
 }
 
 // Load modules.config for DSL2 module specific options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -26,7 +26,7 @@
           "format": "directory-path",
           "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
           "fa_icon": "fas fa-folder-open",
-          "default": "results/"
+          "default": "results"
         },
         "email": {
           "type": "string",