fix node deprecation warnings

PGScatalog · Mar 4, 2024 · cf16c0e · cf16c0e
1 parent e4fa3b0
commit cf16c0e
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Showing 8 changed files with 29 additions and 29 deletions.
diff --git a/.github/workflows/ancestry-conda.yml b/.github/workflows/ancestry-conda.yml
@@ -24,7 +24,7 @@ jobs:
           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

diff --git a/.github/workflows/ancestry-vcf.yml b/.github/workflows/ancestry-vcf.yml
@@ -32,11 +32,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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
@@ -99,11 +99,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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

diff --git a/.github/workflows/ancestry.yml b/.github/workflows/ancestry.yml
@@ -32,11 +32,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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
@@ -93,11 +93,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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

diff --git a/.github/workflows/module.yml b/.github/workflows/module.yml
@@ -29,11 +29,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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 }}
@@ -77,11 +77,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v3
 
-      - 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 }}
@@ -93,7 +93,7 @@ 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 }}

diff --git a/.github/workflows/preload-docker.yml b/.github/workflows/preload-docker.yml
@@ -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 }}
diff --git a/.github/workflows/preload-reference.yml b/.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

diff --git a/.github/workflows/preload-singularity.yml b/.github/workflows/preload-singularity.yml
@@ -19,7 +19,7 @@ jobs:
 
       - 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 }}
diff --git a/.github/workflows/standard-test.yml b/.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 }}