use local data for pytest

tests/config/nextflow.config

@@ -46,7 +46,7 @@ if ("$PROFILE" == "singularity") {
 conda { createTimeout = "120 min" }
 
 // Load test_data.config containing paths to test data
-// includeConfig 'test_data.config'
+includeConfig 'test_data.config'
 
 manifest {
     nextflowVersion = '!>=21.10.3'

tests/config/test_data.config

@@ -0,0 +1,5 @@
+params {
+    input  = "$projectDir/assets/examples/samplesheet.csv"
+    scorefile = "$projectDir/assets/examples/scorefiles/PGS001229_22.txt" 
+    target_build = "GRCh37"
+ }

tests/modules/combine/test.yml

@@ -1,5 +1,5 @@
 - name: test combine scorefiles module
-  command: nextflow run ./tests/modules/combine -entry testcombine -c ./tests/config/nextflow.config -profile test --target_build GRCh38
+  command: nextflow run ./tests/modules/combine -entry testcombine -c ./tests/config/nextflow.config --target_build GRCh38
   tags:
     - module
     - combine

tests/modules/download/test.yml

@@ -1,5 +1,5 @@
 - name: pgscatalog test --pgs_id
-  command: nextflow run ./tests/modules/download -entry testaccession -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/download -entry testaccession -c ./tests/config/nextflow.config
   tags:
     - module
     - download
@@ -11,7 +11,7 @@
         - "pgscatalog_utils: 0.4.0"
 
 - name: pgscatalog test --efo_trait --pgp_id and --pgs_id
-  command: nextflow run ./tests/modules/download -entry testmultipleaccessions -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/download -entry testmultipleaccessions -c ./tests/config/nextflow.config
   tags:
     - module
     - download
@@ -27,15 +27,15 @@
         - "pgscatalog_utils: 0.4.0"
 
 - name: pgscatalog test bad accession
-  command: nextflow run ./tests/modules/download -entry testbadaccession -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/download -entry testbadaccession -c ./tests/config/nextflow.config
   tags:
     - module
     - download
     - fast
   exit_code: 1
 
 - name: pgscatalog test good and bad accessions GRCh38
-  command: nextflow run ./tests/modules/download -entry testmixedaccessions -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/download -entry testmixedaccessions -c ./tests/config/nextflow.config
   tags:
     - module
     - download

tests/modules/match/test.yml

@@ -1,6 +1,6 @@
 # IPC files aren't published so can't test
 - name: test match module
-  command: nextflow run ./tests/modules/match -entry testmatch -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/match -entry testmatch -c ./tests/config/nextflow.config
   tags:
     - module
     - match
@@ -11,7 +11,7 @@
         - "pgscatalog_utils: 0.4.0"
 
 - name: test match combine module
-  command: nextflow run ./tests/modules/match -entry testmatchcombine -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/match -entry testmatchcombine -c ./tests/config/nextflow.config
   tags:
     - module
     - match

tests/modules/plink2/relabelbim/test.yml

@@ -1,5 +1,5 @@
 - name: plink2 testrelabelbim
-  command: nextflow run ./tests/modules/plink2/relabelbim -entry testrelabelbim -c ./tests/config/nextflow.config -profile test 
+  command: nextflow run ./tests/modules/plink2/relabelbim -entry testrelabelbim -c ./tests/config/nextflow.config
   tags:
     - plink2
     - fast

tests/modules/plink2/relabelpvar/test.yml

@@ -1,5 +1,5 @@
 - name: plink2 testrelabelpvar
-  command: nextflow run ./tests/modules/plink2/relabelpvar -entry testrelabelpvar -c ./tests/config/nextflow.config -profile test --vzs
+  command: nextflow run ./tests/modules/plink2/relabelpvar -entry testrelabelpvar -c ./tests/config/nextflow.config
   tags:
     - plink2
     - fast
@@ -12,5 +12,4 @@
     - path: output/plink2/GRCh37_test_22.pvar.zst
     - path: output/plink2/versions.yml
       contains:
-        - "plink2: 2.00a3.3"
-
+        - "plink2: 2.00a3.3"    

tests/modules/plink2/score/test.yml

@@ -1,5 +1,5 @@
 - name: plink2 testscore
-  command: nextflow run ./tests/modules/plink2/score -entry testscore -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/score -entry testscore -c ./tests/config/nextflow.config
   tags:
     - module
     - score
@@ -18,7 +18,7 @@
         - "plink2: 2.00a3.3"
 
 - name: plink2 testsmallscore
-  command: nextflow run ./tests/modules/plink2/score -entry testsmallscore -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/score -entry testsmallscore -c ./tests/config/nextflow.config
   tags:
     - module
     - score
@@ -37,7 +37,7 @@
         - "plink2: 2.00a3.3"
 
 - name: plink2 testmultiscore
-  command: nextflow run ./tests/modules/plink2/score -entry testmultiscore -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/score -entry testmultiscore -c ./tests/config/nextflow.config
   tags:
     - module
     - score
@@ -58,7 +58,7 @@
         - "plink2: 2.00a3.3"
 
 - name: plink2 testsmallmultiscore
-  command: nextflow run ./tests/modules/plink2/score -entry testsmallmultiscore -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/score -entry testsmallmultiscore -c ./tests/config/nextflow.config
   tags:
     - module
     - score
@@ -79,7 +79,7 @@
         - "plink2: 2.00a3.3"
 
 - name: plink2 testmultiscorefail
-  command: nextflow run ./tests/modules/plink2/score -entry testmultiscorefail -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/score -entry testmultiscorefail -c ./tests/config/nextflow.config
   tags:
     - module
     - score

tests/modules/plink2/vcf/test.yml

@@ -1,5 +1,5 @@
 - name: plink2 vcf
-  command: nextflow run ./tests/modules/plink2/vcf -entry testvcf -c ./tests/config/nextflow.config -profile test
+  command: nextflow run ./tests/modules/plink2/vcf -entry testvcf -c ./tests/config/nextflow.config
   tags:
     - module
     - plink2

tests/subworkflows/test_apply_score.yml

@@ -1,6 +1,6 @@
 # get a scores with two columns in output (test profile + PGS001229) for custom test
 - name: test apply score subworkflow
-  command: nextflow run main.nf -profile test --only_score -c ./tests/config/nextflow.config --pgs_id PGS001229 --min_overlap 0
+  command: nextflow run main.nf --only_score -c ./tests/config/nextflow.config --pgs_id PGS001229 --min_overlap 0
   tags:
     - applyscore
     - subworkflow
@@ -14,9 +14,8 @@
     - path: output/plink2/cineca_22_additive_0.sscore.vars
     - path: output/score/aggregated_scores.txt.gz
 
-# TODO: fix overlap -> 1 in pgscatalog_utils
 - name: test perfect apply score
-  command: nextflow run main.nf -profile test --only_score -c ./tests/config/nextflow.config --scorefile ./tests/subworkflows/perfect.txt 
+  command: nextflow run main.nf --only_score -c ./tests/config/nextflow.config --scorefile ./tests/subworkflows/perfect.txt 
   tags:
     - applyscore
     - subworkflow

tests/subworkflows/test_input_subworkflow.yml

@@ -1,5 +1,5 @@
 - name: test input check subworkflow
-  command: nextflow run main.nf -profile test --only_input -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --only_input -c ./tests/config/nextflow.config
   tags:
     - inputcheck
     - subworkflow
@@ -9,7 +9,7 @@
     - path: output/combine/scorefiles.txt.gz
 
 - name: test input check subworkflow with PGS catalog API 
-  command: nextflow run main.nf -profile test --pgs_id PGS001229 --only_input -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --pgs_id PGS001229 --only_input -c ./tests/config/nextflow.config
   tags:
     - inputcheck
     - subworkflow
@@ -20,7 +20,7 @@
     - path: output/combine/scorefiles.txt.gz
 
 - name: test input check subworkflow with PGS catalog API and whitespace
-  command: nextflow run main.nf -profile test --pgs_id "PGS001229, PGS000802" --only_input  -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --pgs_id "PGS001229, PGS000802" --only_input  -c ./tests/config/nextflow.config
   tags:
     - inputcheck
     - subworkflow

tests/subworkflows/test_liftover_run.yml

@@ -1,5 +1,5 @@
 - name: test input check subworkflow with liftover 38to37
-  command: nextflow run main.nf -profile test --only_input --pgs_id PGS000193 --liftover --target_build GRCh37 -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
+  command: nextflow run main.nf --only_input --pgs_id PGS000193 --liftover --target_build GRCh37 -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
   tags:
     - liftover
     - subworkflow
@@ -12,7 +12,7 @@
         - "pgscatalog_utils: 0.4.0"
 
 - name: test input check subworkflow with liftover 37to38
-  command: nextflow run main.nf -profile test --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
+  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
   tags:
     - liftover
     - subworkflow

tests/subworkflows/test_make_compatible.yml

@@ -1,5 +1,5 @@
 - name: test make compatible subworkflow with bfile
-  command: nextflow run main.nf -profile test --input ./assets/examples/samplesheet_bfile.csv --only_compatible -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --input ./assets/examples/samplesheet_bfile.csv --only_compatible -c ./tests/config/nextflow.config
   tags:
     - makecompatible
     - subworkflow
@@ -13,7 +13,7 @@
     - path: output/plink2/GRCh37_cineca_22.vmiss.gz
 
 - name: test make compatible subworkflow with vcf
-  command: nextflow run main.nf -profile test --input ./assets/examples/samplesheet_vcf.csv --only_compatible  -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --input ./assets/examples/samplesheet_vcf.csv --only_compatible  -c ./tests/config/nextflow.config
   tags:
     - makecompatible
     - subworkflow
@@ -27,7 +27,7 @@
     - path: output/plink2/GRCh37_vcf_22.vmiss.gz      
 
 - name: test make compatible subworkflow with pfile
-  command: nextflow run main.nf -profile test --only_compatible -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --only_compatible -c ./tests/config/nextflow.config
   tags:
     - makecompatible
     - subworkflow

tests/subworkflows/test_match.yml

@@ -1,5 +1,5 @@
 - name: test match subworkflow
-  command: nextflow run main.nf -profile test --only_match -c ./tests/config/nextflow.config
+  command: nextflow run main.nf --only_match -c ./tests/config/nextflow.config
   tags:
     - match
     - subworkflow