Merge pull request #966 from nf-core/dev

Dev -> Master for 3.11 release
nf-core · Mar 30, 2023 · 48fb9b4 · 48fb9b4
2 parents 6e1e448 + fbffe86
commit 48fb9b4
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,9 +35,33 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: rnaseq3_10-test-data
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: rnaseq3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
@@ -58,18 +82,43 @@ jobs:
           - "--bam_csi_index"
           - "--save_align_intermeds --save_reference"
           - "--featurecounts_group_type false"
+          - "--trimmer fastp"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: rnaseq3_10-test-data
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: rnaseq3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
@@ -84,14 +133,38 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: rnaseq3_10-test-data
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: rnaseq3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with RSEM STAR and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   hisat2:
     name: Test HISAT2 with workflow parameters
@@ -106,14 +179,38 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: rnaseq3_10-test-data
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: rnaseq3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with HISAT2 and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
 
   salmon:
     name: Test Salmon with workflow parameters
@@ -128,11 +225,35 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Cache test data
+        id: cache-testdata
+        uses: actions/cache@v3
+        with:
+          path: test-datasets/
+          key: rnaseq3_10-test-data
+
+      - name: Check out test data
+        if: steps.cache-testdata.outputs.cache-hit != 'true'
+        uses: actions/checkout@v3
+        with:
+          repository: nf-core/test-datasets
+          ref: rnaseq3
+          path: test-datasets/
+
+      - name: Replace remote paths in samplesheets
+        run: |
+          for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
+            sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
+            echo "========== $f ============"
+            cat $f
+            echo "========================================"
+          done;
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
       - name: Run pipeline with Salmon and various parameters
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
@@ -0,0 +1,94 @@
+name: full-sized tests on cloud providers
+run-name: Submitting workflow to all cloud providers using full sized data
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+    inputs:
+      platform:
+        description: "Platform to run test"
+        required: true
+        default: "all"
+        type: choice
+        options:
+          - all
+          - aws
+          - azure
+          - gcp
+jobs:
+  run-full-tests-on-aws:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["star_salmon", "star_rsem"]
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "aws_rnaseq_full_${{ matrix.aligner }}"
+          profiles: test_full_aws
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
+            }
+          wait: false
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-full-tests-on-gcp:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["star_salmon", "star_rsem"]
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_GCP_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_GCP }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "gcp_rnaseq_full_${{ matrix.aligner }}"
+          profiles: test_full_gcp
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
+            }
+          wait: false
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log
+  run-full-tests-on-azure:
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["star_salmon", "star_rsem"]
+    steps:
+      - uses: seqeralabs/action-tower-launch@v1
+        with:
+          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
+          compute_env: ${{ secrets.TOWER_CE_AZURE_CPU }}
+          workdir: "${{ secrets.TOWER_BUCKET_AZURE }}/work/rnaseq/work-${{ github.sha }}"
+          run_name: "azure_rnaseq_full_${{ matrix.aligner }}"
+          profiles: test_full_azure
+          parameters: |
+            {
+                "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
+                "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
+            }
+          wait: false
+      - uses: actions/upload-artifact@v3
+        with:
+          name: Tower debug log file
+          path: tower_action_*.log