Merge pull request #374 from maxulysse/dev_2.7.1

Prepare release 2.7.1
nf-core · Jun 14, 2021 · 68b9930 · 68b9930
2 parents 7ccfb36 + 3c98945
commit 68b9930
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
     steps:
       - checkout
       - setup_remote_docker
@@ -20,28 +20,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   vepgrch37: &buildvep
     docker:
@@ -50,7 +50,7 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
     steps:
       - checkout
       - setup_remote_docker
@@ -67,31 +67,31 @@ jobs:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
-      SAREK_TAG: 2.7
+      SAREK_TAG: 2.7.1
 
 workflows:
   version: 2

diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
@@ -3,3 +3,4 @@ version: 1.2
 workflows:
   - subclass: nfl
     primaryDescriptorPath: /nextflow.config
+    publish: True
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -69,7 +69,7 @@ If you wish to contribute a new step, please use the following coding standards:
 2. Write the process block (see below).
 3. Define the output channel if needed (see below).
 4. Add any new flags/options to `nextflow.config` with a default (see below).
-5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`)
+5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`).
 6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter).
 7. Add sanity checks for all relevant parameters.
 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`.
@@ -87,7 +87,7 @@ Once there, use `nf-core schema build .` to add to `nextflow_schema.json`.
 
 ### Default processes resource requirements
 
-Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
+Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
 The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
 

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -3,8 +3,7 @@ name: Bug report
 about: Report something that is broken or incorrect
 title: "[BUG]"
 labels: bug
-assignees: MaxUlysse
-
+assignees: maxulysse
 ---
 
 <!--
@@ -21,7 +20,7 @@ Please delete this text and anything that's not relevant from the template below
 I have checked the following places for your error:
 
 - [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-- [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/nf-core/sarek/usage)
+- [ ] [nf-core/sarek pipeline documentation](https://nf-co.re/sarek/usage)
 
 ## Description of the bug
 
@@ -58,9 +57,9 @@ Have you provided the following extra information/files:
 
 ## Container engine
 
-- Engine: <!-- [e.g. Conda, Docker, Singularity or Podman] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
-- Image tag: <!-- [e.g. nfcore/sarek:2.6] -->
+- Image tag: <!-- [e.g. nfcore/sarek:2.7] -->
 
 ## Additional context
 

diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
@@ -3,8 +3,7 @@ name: Feature request
 about: Suggest an idea for the nf-core/sarek pipeline
 title: "[FEATURE]"
 labels: enhancement
-assignees: MaxUlysse
-
+assignees: maxulysse
 ---
 
 <!--

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -10,14 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
 -->
+<!-- markdownlint-disable ul-indent -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-  - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
-  - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-  - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+    - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py`
+    - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
+    - [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint .`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

diff --git a/.github/markdownlint.yml b/.github/markdownlint.yml
@@ -5,9 +5,8 @@ no-duplicate-header:
     siblings_only: true
 no-inline-html:
     allowed_elements:
-        - a
-        - details
         - img
-        - kbd
         - p
+        - kbd
+        - details
         - summary
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -9,6 +9,16 @@ on:
     types: [completed]
   workflow_dispatch:
 
+
+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 }}
+
+
 jobs:
   run-awstest:
     name: Run AWS full tests
@@ -27,13 +37,6 @@ jobs:
         # 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 \

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -6,6 +6,16 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 
+
+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 }}
+
+
 jobs:
   run-awstest:
     name: Run AWS tests
@@ -20,13 +30,9 @@ jobs:
       - name: Install awscli
         run: conda install -c conda-forge awscli
       - name: Start AWS batch job
-        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 }}
+        # TODO nf-core: You can customise CI pipeline run tests as required
+        # For example: adding multiple test runs with different parameters
+        # Remember that you can parallelise this by using strategy.matrix
         run: |
           aws batch submit-job \
           --region eu-west-1 \

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/sarek'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/sarek ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
 
       # If the above check failed, post a comment on the PR explaining the failure
@@ -23,14 +23,24 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
+            ## This PR is against the `master` branch :x:
+
+            * Do not close this PR
+            * Click _Edit_ and change the `base` to `dev`
+            * This CI test will remain failed until you push a new commit
+
+            ---
+
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
             The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch.
+            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
+            Note that even after this, the test will continue to show as failing until you push a new commit.
 
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
+
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,6 +8,9 @@ on:
   release:
     types: [published]
 
+# Uncomment if we need an edge release of Nextflow again
+# env: NXF_EDGE: 1
+
 jobs:
   test:
     name: Run workflow tests
@@ -33,13 +36,13 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/sarek:2.7
+        run: docker build --no-cache . -t nfcore/sarek:2.7.1
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.7
+          docker tag nfcore/sarek:dev nfcore/sarek:2.7.1
 
       - name: Install Nextflow
         env:
@@ -71,8 +74,8 @@ jobs:
           NXF_VER: '20.04.0'
       - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:2.7
-          docker pull nfcore/sarek${{ matrix.tools }}:2.7.${{ matrix.species }}
+          docker pull nfcore/sarek:2.7.1
+          docker pull nfcore/sarek${{ matrix.tools }}:2.7.1.${{ matrix.species }}
       - name: Run annotation test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
 
@@ -93,7 +96,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.7
+        run: docker pull nfcore/sarek:2.7.1
       - name: Get test data
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test
@@ -121,9 +124,9 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.7
+        run: docker pull nfcore/sarek:2.7.1
       - 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
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_qc all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
   profile:
     env:
@@ -142,7 +145,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.7
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
 
@@ -163,7 +166,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.7
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
 
@@ -194,6 +197,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:2.7
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.tool }} test
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}