diff --git a/conf/modules.config b/conf/modules.config index 81ebf32f..1f345793 100644 --- 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 index fac6ef15..fbf645ed 100644 --- 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 index 0dcf4c16..ba6c16dc 100644 --- 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" \ No newline at end of file + - "pgscatalog.core: 0.2.2" \ No newline at end of file diff --git a/tests/modules/download/test.yml b/tests/modules/download/test.yml index 0d2bde30..54323166 100644 --- 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 index 5db1804e..d0c41127 100644 --- 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 index 5575cf2f..6453caff 100644 --- 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 index 637f37cf..9c322606 100644 --- 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 index 1aa3f90a..e02c2010 100644 --- 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"