v2.0.0-alpha.1

.github/workflows/standard-test.yml

@@ -27,9 +27,11 @@ jobs:
         nxf_ver: ['22.10.0', 'latest']
 
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
+      - name: Extract branch name
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+        id: extract_branch
+
       - uses: nf-core/setup-nextflow@v1
         with:
           version: ${{ matrix.nxf_ver }}
@@ -49,7 +51,7 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }}
+          nextflow run pgscatalog/pgsc_calc -r ${{ steps.extract_branch.outputs.branch }} -profile ${{ matrix.test_profile}},${{ matrix.profile }}
 
   singularity:
     if: ${{ inputs.singularity }}
@@ -62,9 +64,11 @@ jobs:
         nxf_ver: ['22.10.0', 'latest']
 
     steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
+      - name: Extract branch name
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+        id: extract_branch
+
       - uses: nf-core/setup-nextflow@v1
         with:
           version: ${{ matrix.nxf_ver }}
@@ -90,4 +94,4 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_profile}},${{ matrix.profile }}
+          nextflow run pgscatalog/pgsc_calc -r ${{ steps.extract_branch.outputs.branch }} -profile ${{ matrix.test_profile}},${{ matrix.profile }}

conf/modules.config

@@ -61,9 +61,9 @@ process {
     withLabel: report {
         ext.conda = "$projectDir/environments/report/environment.yml"
         ext.singularity = 'oras://dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/singularity/report'
-        ext.singularity_version = ':dev'
+        ext.singularity_version = ':2.0'
         ext.docker = 'dockerhub.ebi.ac.uk/gdp-public/pgsc_calc/report'
-        ext.docker_version = ':dev'
+        ext.docker_version = ':2.0'
     }
 
     withLabel: pyyaml {

conf/test.config

@@ -19,9 +19,13 @@ params {
     max_memory = '6.GB'
     max_time   = '6.h'
 
-    input  = "$projectDir/assets/examples/samplesheet.csv"
-    scorefile = "$projectDir/assets/examples/scorefiles/PGS001229_22.txt" 
+    input  = "https://gitlab.ebi.ac.uk/nebfield/test-datasets/-/raw/master/pgsc_calc/input_v2.json"
+    format = "json"
+    scorefile = "https://gitlab.ebi.ac.uk/nebfield/test-datasets/-/raw/master/pgsc_calc/PGS001229_22.txt" 
+
+    // TODO: fix local tests with CSV
+    // input  = "$projectDir/assets/examples/samplesheet.csv"
+    // scorefile = "$projectDir/assets/examples/scorefiles/PGS001229_22.txt" 
     outdir = "$projectDir/results"
     target_build = "GRCh37"
-    skip_ancestry = true
 }

conf/test_json.config

@@ -12,5 +12,4 @@ params {
     scorefile = "https://gitlab.ebi.ac.uk/nebfield/test-datasets/-/raw/master/pgsc_calc/PGS001229_22.txt" 
     outdir = "$projectDir/results"
     target_build = "GRCh37"
-    skip_ancestry = true
 }

docs/changelog.rst

@@ -8,8 +8,17 @@ will only occur in major versions with changes noted in this changelog.
 
 .. _`semantic versioning`: https://semver.org/
 
+pgsc_calc v2.0.0-alpha.1 (2023-08-11)
+-------------------------------------
+
+This patch fixes a bug when running the workflow directly from github with the
+test profile (i.e. without cloning first). Thanks to `@staedlern`_ for reporting the
+problem.
+
+.. _`@staedlern`: https://github.com/PGScatalog/pgsc_calc/issues/151
+
 pgsc_calc v2.0.0-alpha (2023-08-08)
------------------------------
+-----------------------------------
 
 This major release features breaking changes to samplesheet structure to provide
 more flexible support for extra genomic file types in the future. Two major new

tests/ancestry/test.yml

@@ -12,7 +12,8 @@
       --target_build GRCh38 \
       --pgs_id PGS001229 \
       --min_overlap 0.50 \
-      --target_build GRCh38
+      --target_build GRCh38 \
+      --scorefile false
     "
   tags:
     - ancestry

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