v2.0.0-alpha.5

.github/workflows/ancestry-conda.yml

@@ -16,15 +16,15 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set environment variables
         run: |
           echo "ANCESTRY_REF_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
           echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
 
       - name: Restore reference data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
@@ -52,7 +52,7 @@ jobs:
           sudo mv nextflow /usr/local/bin/
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'

.github/workflows/ancestry-vcf.yml

@@ -30,13 +30,13 @@ jobs:
           echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
 
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore docker images
         id: restore-docker
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: ${{ runner.temp }}/docker
           key: ${{ inputs.container-cache-key }}
@@ -48,7 +48,7 @@ jobs:
           find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;
 
       - name: Restore reference data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
@@ -65,7 +65,7 @@ jobs:
         run: plink2 --pfile ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL vzs --export vcf bgz --out ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'
@@ -97,13 +97,13 @@ jobs:
           echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
 
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore singularity setup
         id: restore-singularity-setup
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
           key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
@@ -115,13 +115,13 @@ jobs:
 
       - name: Restore singularity container images
         id: restore-singularity
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
           key: ${{ inputs.container-cache-key }}
 
       - name: Restore reference data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
@@ -138,7 +138,7 @@ jobs:
         run: plink2 --pfile ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL vzs --export vcf bgz --out ${ANCESTRY_TARGET_DIR}/GRCh38_HAPNEST_TARGET_ALL
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'

.github/workflows/ancestry.yml

@@ -30,13 +30,13 @@ jobs:
           echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
 
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore docker images
         id: restore-docker
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: ${{ runner.temp }}/docker
           key: ${{ inputs.container-cache-key }}
@@ -48,7 +48,7 @@ jobs:
           find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;
 
       - name: Restore reference data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
@@ -59,7 +59,7 @@ jobs:
           fail-on-cache-miss: true
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'
@@ -91,13 +91,13 @@ jobs:
           echo "ANCESTRY_TARGET_DIR=$RUNNER_TEMP" >> $GITHUB_ENV
 
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore singularity setup
         id: restore-singularity-setup
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
           key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
@@ -109,13 +109,13 @@ jobs:
 
       - name: Restore singularity container images
         id: restore-singularity
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
           key: ${{ inputs.container-cache-key }}
 
       - name: Restore reference data
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen
@@ -126,7 +126,7 @@ jobs:
           fail-on-cache-miss: true
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'

.github/workflows/conda.yml

@@ -32,7 +32,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - uses: conda-incubator/setup-miniconda@v2
         with:  

.github/workflows/module.yml

@@ -27,13 +27,13 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore docker images
         id: restore-docker
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: ${{ runner.temp }}/docker
           key: ${{ inputs.cache-key }}
@@ -45,7 +45,7 @@ jobs:
           find ${{ runner.temp }}/docker/ -name '*.tar' -exec sh -c 'docker load < {}' \;
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'
@@ -75,13 +75,13 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
 
       - name: Restore singularity setup
         id: restore-singularity-setup
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
           key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
@@ -93,13 +93,13 @@ jobs:
 
       - name: Restore singularity container images
         id: restore-singularity
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
           key: ${{ inputs.cache-key }}
 
       - name: Set up test requirements
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: '3.10'
           cache: 'pip'

.github/workflows/preload-docker.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Pull and save docker
         run: |
@@ -22,7 +22,7 @@ jobs:
 
       - name: Save docker
         id: cache-docker
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ runner.temp }}/docker
           key: docker-${{ github.sha }}

.github/workflows/preload-reference.yml

@@ -17,7 +17,7 @@ jobs:
 
       - name: Cache reference data
         id: cache-ref
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: |
             ${{ env.ANCESTRY_TARGET_DIR }}/GRCh38_HAPNEST_TARGET_ALL.pgen

.github/workflows/preload-singularity.yml

@@ -15,11 +15,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Cache singularity setup
         id: cache-singularity-setup
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
           key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
@@ -44,7 +44,7 @@ jobs:
 
       - name: Cache singularity images
         id: cache-singularity-pull
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
           key: singularity-${{ github.sha }}

.github/workflows/standard-test.yml

@@ -33,13 +33,13 @@ jobs:
         run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
         id: extract_branch
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.nxf_ver }}
 
       - name: Restore docker images
         id: restore-docker
-        uses: actions/cache/restore@v3
+        uses: actions/cache/restore@v4
         with:
           path: ${{ runner.temp }}/docker
           key: ${{ inputs.cache-key }}
@@ -70,13 +70,13 @@ jobs:
         run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
         id: extract_branch
 
-      - uses: nf-core/setup-nextflow@v1
+      - uses: nf-core/setup-nextflow@v2
         with:
           version: ${{ matrix.nxf_ver }}
 
       - name: Restore singularity setup
         id: restore-singularity-setup
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: /opt/hostedtoolcache/singularity/${{ env.SINGULARITY_VERSION }}/x64
           key: ${{ runner.os }}-singularity-${{ env.SINGULARITY_VERSION }}
@@ -88,7 +88,7 @@ jobs:
 
       - name: Restore singularity container images
         id: restore-singularity
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ${{ env.NXF_SINGULARITY_CACHEDIR }}
           key: ${{ inputs.cache-key }}

.gitignore

@@ -6,3 +6,7 @@ results/
 testing/
 testing*
 *.pyc
+.Rproj.user
+assets/report/renv/
+assets/report/report.Rproj
+.Rprofile

assets/examples/samplesheet.json

@@ -1 +1,11 @@
-[{"sampleset":"cineca_synthetic_subset","vcf_path":null,"chrom":22,"bed":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bim","bim":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bed","fam":"https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.fam"}]
+[
+    {
+        "sampleset": "hgdp",
+        "chrom": null,
+        "vcf_import_dosage": false,
+        "geno": "https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bed",
+        "pheno": "https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.fam",
+        "variants": "https:\/\/gitlab.ebi.ac.uk\/nebfield\/test-datasets\/-\/raw\/master\/pgsc_calc\/cineca_synthetic_subset.bim",
+        "format": "bfile"
+    }
+]

assets/examples/scorefiles/customgrch37.txt

@@ -0,0 +1,6 @@
+#pgs_name=testlift
+#trait_reported=test
+#genome_build=GRCh37
+chr_name	chr_position	effect_allele	other_allele	effect_weight
+1	4859488	A	G	-0.0504139458332669
+1	5297845	G	A	0.040436175688854

assets/examples/scorefiles/customgrch38.txt

@@ -0,0 +1,6 @@
+#pgs_name=test
+#trait_reported=test
+#genome_build=GRCh38
+chr_name	chr_position	effect_allele	other_allele	effect_weight
+1	4799428	A	G	-0.0504139458332669
+1	5237785	G	A	0.040436175688854