bump pgscatalog-utils version

PGScatalog · Jul 29, 2024 · 9f675c0 · 9f675c0
1 parent 913b191
commit 9f675c0
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Showing 8 changed files with 14 additions and 11 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -38,8 +38,8 @@ process {
         ext.conda = "$projectDir/environments/pgscatalog_utils/environment.yml"
         ext.docker = 'ghcr.io/pgscatalog/pygscatalog'
         ext.singularity = 'oras://ghcr.io/pgscatalog/pygscatalog'
-        ext.docker_version = ':pgscatalog-utils-1.1.2'
-        ext.singularity_version = ':pgscatalog-utils-1.1.2-singularity'
+        ext.docker_version = ':pgscatalog-utils-1.2.0'
+        ext.singularity_version = ':pgscatalog-utils-1.2.0-singularity'
     }
 
     withLabel: plink2 {

diff --git a/environments/pgscatalog_utils/environment.yml b/environments/pgscatalog_utils/environment.yml
@@ -3,4 +3,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-- pgscatalog-utils=1.1.2
+- pgscatalog-utils=1.2.0
diff --git a/tests/modules/combine/test.yml b/tests/modules/combine/test.yml
@@ -14,4 +14,4 @@
         - "effect_weight"
     - path: output/combine/versions.yml
       contains:
-        - "pgscatalog.core: 0.2.1"
+        - "pgscatalog.core: 0.2.2"
diff --git a/tests/modules/download/test.yml b/tests/modules/download/test.yml
@@ -8,7 +8,7 @@
     - path: output/download/PGS000001_hmPOS_GRCh37.txt.gz
     - path: output/download/versions.yml
       contains:
-        - "pgscatalog.core: 0.2.1"
+        - "pgscatalog.core: 0.2.2"
 
 - 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.core: 0.2.1"
+        - "pgscatalog.core: 0.2.2"
 
 - name: pgscatalog test bad accession
   command: nextflow run ./tests/modules/download -entry testbadaccession -c ./tests/config/nextflow.config

diff --git a/tests/modules/match/test.yml b/tests/modules/match/test.yml
@@ -7,7 +7,7 @@
   files:
     - path: output/test/match/versions.yml
       contains:
-        - "pgscatalog.match: 0.2.2"
+        - "pgscatalog.match: 0.2.3"
 # can't test IPC output (not published)        
 
 - name: test match combine module
@@ -20,7 +20,7 @@
   files:
     - path: output/test/match/versions.yml
       contains:
-        - "pgscatalog.match: 0.2.2"
+        - "pgscatalog.match: 0.2.3"
     - path: output/test/match/test_ALL_additive_0.scorefile.gz           
       contains:
         - "PGS001229"     

diff --git a/tests/subworkflows/test_apply_score.py b/tests/subworkflows/test_apply_score.py
@@ -19,7 +19,7 @@ def test_aggregated_scores(workflow_dir):
 
     assert not df.isnull().any().any(), "Missing values in aggregated scores"
 
-    cols = ["sampleset", "IID", "PGS", "SUM", "DENOM", "AVG"]
+    cols = ["sampleset", "FID", "IID", "PGS", "SUM", "DENOM", "AVG"]
     assert cols == list(df.columns), "Missing columns"
     assert (
         len(

diff --git a/tests/subworkflows/test_apply_score.yml b/tests/subworkflows/test_apply_score.yml
@@ -16,6 +16,9 @@
         - "IID"
         - "PGS"
         - "SUM"
+    - path: output/score/versions.yml
+      contains:
+        - "pgscatalog.calc: 0.2.2"
       must_not_contain:
         - "percentile_MostSimilarPop"
         - "Z_MostSimilarPop"

diff --git a/tests/subworkflows/test_liftover_run.yml b/tests/subworkflows/test_liftover_run.yml
@@ -11,7 +11,7 @@
       - "5297845"
     - path: output/combine/versions.yml      
       contains:
-        - "pgscatalog.core: 0.2.1"
+        - "pgscatalog.core: 0.2.2"
 
 - name: test input check subworkflow with liftover 37to38
   command: nextflow run main.nf --only_input --scorefile ./assets/examples/scorefiles/customgrch37.txt --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
@@ -26,4 +26,4 @@
       - "5237785"
     - path: output/combine/versions.yml
       contains:
-        - "pgscatalog.core: 0.2.1"
+        - "pgscatalog.core: 0.2.2"