Merge pull request #166 from PGScatalog/dev

2.0.0-alpha.2

conf/modules.config

@@ -38,8 +38,8 @@ process {
         ext.conda = "$projectDir/environments/pgscatalog_utils/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/pgscatalog_utils'
         ext.singularity = 'oras://ghcr.io/pgscatalog/pgscatalog_utils'
-        ext.docker_version = ':v0.4.0'
-        ext.singularity_version = ':v0.4.0-singularity'
+        ext.docker_version = ':v0.4.1'
+        ext.singularity_version = ':v0.4.1-singularity'
     }
 
     withLabel: plink2 {

environments/pgscatalog_utils/environment.yml

@@ -3,4 +3,4 @@ dependencies:
 - python=3.10
 - pip
 - pip:
-    - pgscatalog_utils==0.4.0
+    - pgscatalog_utils==0.4.1

nextflow.config

@@ -209,7 +209,7 @@ manifest {
     description     = 'The Polygenic Score Catalog Calculator is a nextflow pipeline for polygenic score calculation'
     mainScript      = 'main.nf'
     nextflowVersion = '>=22.10.0'
-    version         = '2.0.0-alpha.1'
+    version         = '2.0.0-alpha.2'
 }
 
 // Load modules.config for DSL2 module specific options

tests/modules/combine/test.yml

@@ -15,6 +15,6 @@
         - "effect_type"
     - path: output/combine/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
 
 

tests/modules/download/test.yml

@@ -8,7 +8,7 @@
     - path: output/download/PGS000001_hmPOS_GRCh37.txt.gz
     - path: output/download/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
 
 - name: pgscatalog test --efo_trait --pgp_id and --pgs_id
   command: nextflow run ./tests/modules/download -entry testmultipleaccessions -c ./tests/config/nextflow.config
@@ -24,7 +24,7 @@
     - path: output/download/PGS002054_hmPOS_GRCh37.txt.gz
     - path: output/download/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
 
 - name: pgscatalog test bad accession
   command: nextflow run ./tests/modules/download -entry testbadaccession -c ./tests/config/nextflow.config
@@ -44,4 +44,4 @@
     - path: output/download/PGS000001_hmPOS_GRCh38.txt.gz
     - path: output/download/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"

tests/modules/match/test.yml

@@ -8,7 +8,7 @@
   files:
     - path: output/test/match/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
 
 - name: test match combine module
   command: nextflow run ./tests/modules/match -entry testmatchcombine -c ./tests/config/nextflow.config
@@ -20,7 +20,7 @@
   files:
     - path: output/combine/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
     - path: output/combine/scorefiles.txt.gz
       contains:
         - "effect_allele"

tests/subworkflows/test_liftover_run.yml

@@ -9,7 +9,7 @@
     - path: output/combine/scorefiles.txt.gz
     - path: output/combine/versions.yml      
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"
 
 - name: test input check subworkflow with liftover 37to38
   command: nextflow run main.nf --only_input --pgs_id PGS001229 --liftover --target_build GRCh38 -c ./tests/config/nextflow.config --hg19_chain https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz --hg38_chain https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
@@ -22,4 +22,4 @@
     - path: output/combine/scorefiles.txt.gz
     - path: output/combine/versions.yml
       contains:
-        - "pgscatalog_utils: 0.4.0"
+        - "pgscatalog_utils: 0.4.1"