Merge pull request #222 from MaxUlysse/2.6.1

2.6.1
nf-core · Jun 23, 2020 · bce378e · bce378e
2 parents 75fe254 + e6b97db
commit bce378e
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Showing 17 changed files with 1,662 additions and 1,546 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
     steps:
       - checkout
       - setup_remote_docker
@@ -20,28 +20,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   vepgrch37: &buildvep
     docker:
@@ -50,7 +50,7 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
     steps:
       - checkout
       - setup_remote_docker
@@ -59,38 +59,39 @@ jobs:
           no_output_timeout: 3h
       - run:
           command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:${SAREK_TAG}.${GENOME}
+          no_output_timeout: 30m
 
   vepgrch38:
     << : *buildvep
     environment:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
-      SAREK_TAG: 2.6
+      SAREK_TAG: "2.6.1"
 
 workflows:
   version: 2

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -0,0 +1,40 @@
+name: nf-core AWS full test
+# This workflow is triggered on push to the master branch and on published releases.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  run-awstest:
+    if: github.repository == 'nf-core/sarek'
+    name: Run AWS full tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Setup Miniconda
+        uses: goanpeca/[email protected]
+        with:
+          auto-update-conda: true
+          python-version: 3.7
+      - name: Install awscli
+        run: conda install -c conda-forge awscli
+      - name: Start AWS batch job
+        # TODO nf-core: You can customise AWS full pipeline tests as required
+        # Add full size test data (but still relatively small datasets for few samples) 
+        # on the `test_full.config` test runs with only one set of parameters
+        # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command
+        env:
+          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
+          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
+          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
+          AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
+          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
+          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
+        run: |
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-sarek \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -6,11 +6,10 @@ on:
   push:
     branches:
       - master
-  release:
-    types: [published]
 
 jobs:
   run-awstest:
+    if: github.repository == 'nf-core/sarek'
     name: Run AWS test
     runs-on: ubuntu-latest
     steps:
@@ -23,8 +22,16 @@ jobs:
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
         env:
-          AWS_ACCESS_KEY_ID: ${{secrets.AWS_KEY_ID}}
-          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_KEY_SECRET}}
-          TOWER_ACCESS_TOKEN: ${{secrets.TOWER_ACCESS_TOKEN}}
+          AWS_ACCESS_KEY_ID: ${{secrets.AWS_ACCESS_KEY_ID}}
+          AWS_SECRET_ACCESS_KEY: ${{secrets.AWS_SECRET_ACCESS_KEY}}
+          TOWER_ACCESS_TOKEN: ${{secrets.AWS_TOWER_TOKEN}}
+          AWS_JOB_DEFINITION: ${{secrets.AWS_JOB_DEFINITION}}
+          AWS_JOB_QUEUE: ${{secrets.AWS_JOB_QUEUE}}
+          AWS_S3_BUCKET: ${{secrets.AWS_S3_BUCKET}}
         run: |
-          aws batch submit-job --region eu-west-1 --job-name nf-core-sarek --job-queue 'default-8b3836e0-5eda-11ea-96e5-0a2c3f6a2a32' --job-definition nextflow --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://nf-core-awsmegatests/sarek/results-'"${GITHUB_SHA}"' -w s3://nf-core-awsmegatests/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' 
+          aws batch submit-job \
+          --region eu-west-1 \
+          --job-name nf-core-sarek \
+          --job-queue $AWS_JOB_QUEUE \
+          --job-definition $AWS_JOB_DEFINITION \
+          --container-overrides '{"command": ["nf-core/sarek", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/sarek/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/sarek/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}'
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.6
+          docker tag nfcore/sarek:dev nfcore/sarek:2.6.1
       - name: Run test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker
 
@@ -45,8 +45,8 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:2.6
-          docker pull nfcore/sarek${{ matrix.tools }}:2.6.${{ matrix.species }}
+          docker pull nfcore/sarek:2.6.1
+          docker pull nfcore/sarek${{ matrix.tools }}:2.6.1.${{ matrix.species }}
       - name: Run annotation test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
 
@@ -67,7 +67,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.6
+        run: docker pull nfcore/sarek:2.6.1
       - name: Get test data
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test
@@ -95,7 +95,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.6
+        run: docker pull nfcore/sarek:2.6.1
       - name: Run test for minimal genomes
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
@@ -116,7 +116,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.6
+        run: docker pull nfcore/sarek:2.6.1
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
 
@@ -147,6 +147,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.6
+        run: docker pull nfcore/sarek:2.6.1
       - name: Run ${{ matrix.tool }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}