Merge pull request #501 from maxulysse/template-merge-2.3

Template merge tools@2.3

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,7 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/sare
     - [ ] 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`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker` --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: nf-core/tower-action@v3
         # 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
@@ -31,4 +31,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/awstest.yml

@@ -11,7 +11,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: nf-core/tower-action@v3
+
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -24,4 +25,6 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/sarek/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-          pre_run_script: 'export NXF_VER=21.10.3'
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3

.github/workflows/branch.yml

@@ -43,4 +43,3 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-

.github/workflows/ci.yml

@@ -14,7 +14,7 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}
     runs-on: ubuntu-latest

.github/workflows/linting.yml

@@ -13,8 +13,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: actions/setup-node@v2
-        with:
-          node-version: '17'
       - name: Install markdownlint
         run: npm install -g markdownlint-cli
       - name: Run Markdownlint
@@ -52,8 +50,6 @@ jobs:
       - uses: actions/checkout@v2
 
       - uses: actions/setup-node@v2
-        with:
-          node-version: '17'
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -64,14 +60,13 @@ jobs:
   YAML:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
-      - uses: actions/setup-node@v2
+      - name: Checkout
+        uses: actions/checkout@master
+      - name: 'Yamllint'
+        uses: karancode/yamllint-github-action@master
         with:
-          node-version: '17'
-      - name: Install yaml-lint
-        run: npm install -g yaml-lint
-      - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.yamllint.yml
+          yamllint_file_or_dir: '.'
+          yamllint_config_filepath: '.yamllint.yml'
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment
@@ -84,8 +79,9 @@ jobs:
             To keep the code consistent with lots of contributors, we run automated code consistency checks.
             To fix this CI test, please run:
 
-            * Install `yaml-lint`
-                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
+            * Install `yamllint`
+                * Install `yamllint` following [this](https://yamllint.readthedocs.io/en/stable/quickstart.html#installing-yamllint)
+                instructions or alternative install it in your [conda environment](https://anaconda.org/conda-forge/yamllint)
             * Fix the markdown errors
                 * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml") -c ./.yamllint.yml`
                 * Fix any reported errors in your YAML files
@@ -120,7 +116,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools.git@dev
+          pip install nf-core
 
       - name: Run nf-core lint
         env:

.github/workflows/linting_comment.yml

@@ -1,7 +1,7 @@
-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
+
 on:
   workflow_run:
     workflows: ["nf-core linting"]
@@ -26,4 +26,3 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-

.github/workflows/local_modules.yml

@@ -24,7 +24,7 @@ jobs:
       matrix:
         nxf_version: ['21.04.0']
         tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
-        profile: ['docker', 'singularity'] ## 'conda'
+        profile: ['docker', 'singularity']  # 'conda'
     env:
       NXF_ANSI_LOG: false
     steps:

.gitpod.yml

@@ -1,9 +1,9 @@
 image: nfcore/gitpod:latest
 
 vscode:
-  extensions: # based on nf-core.nf-core-extensionpack
+  extensions:  # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore                 # Language support for .gitignore files
-    # - cssho.vscode-svgviewer                 # SVG viewer
+    # - cssho.vscode-svgviewer                 # SVG viewer
     - davidanson.vscode-markdownlint         # Markdown/CommonMark linting and style checking for Visual Studio Code
     - eamodio.gitlens                        # Quickly glimpse into whom, why, and when a line or code block was changed
     - EditorConfig.EditorConfig              # override user/workspace settings with settings found in .editorconfig files

.nf-core.yml

@@ -1,6 +1,7 @@
 repository_type: pipeline
 lint:
   files_unchanged:
+    - .github/PULL_REQUEST_TEMPLATE.md
     - .github/workflows/branch.yml
     - .github/workflows/linting.yml
     - .github/workflows/linting_comment.yml

README.md

@@ -51,20 +51,20 @@ By default, the pipeline currently performs the following:
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/sarek -profile test,YOURPROFILE
+    nextflow run nf-core/sarek -profile test,YOURPROFILE --outdir <OUTDIR>
     ```
 
     Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
 
     > * The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
     > * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-    > * If you are using `singularity` and are persistently observing issues downloading Singularity images directly due to timeout or network issues, then you can use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, you can use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
+    > * If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
     > * If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs.
 
 4. Start running your own analysis!
 
-    ```bash
-    nextflow run nf-core/sarek -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input sample.csv --genome GRCh38
+    ```console
+    nextflow run nf-core/sarek -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input samplesheet.csv --outdir <OUTDIR> --genome GRCh38
     ```
 
 See [usage docs](https://nf-co.re/sarek/usage) for all of the available options when running the pipeline.

assets/multiqc_config.yaml

@@ -15,20 +15,20 @@ report_section_order:
 export_plots: true
 
 top_modules:
-- 'fastqc':
-  name: 'FastQC'
-  path_filters_exclude:
-    - '*trimmed_fastqc*'
-- 'cutadapt'
-- 'fastqc':
-  name: 'FastQC after trimming'
-  info: 'FastQC after applying TrimGalore.'
-  path_filters:
-    - '*trimmed_fastqc*'
-- 'picard'
-- 'gatk'
-- 'samtools'
-- 'qualimap'
-- 'bcftools'
-- 'vcftools'
-- 'snpeff'
+    - 'fastqc':
+      name: 'FastQC'
+      path_filters_exclude:
+          - '*trimmed_fastqc*'
+    - 'cutadapt'
+    - 'fastqc':
+      name: 'FastQC after trimming'
+      info: 'FastQC after applying TrimGalore.'
+      path_filters:
+          - '*trimmed_fastqc*'
+    - 'picard'
+    - 'gatk'
+    - 'samtools'
+    - 'qualimap'
+    - 'bcftools'
+    - 'vcftools'
+    - 'snpeff'

conf/base.config

@@ -1,7 +1,7 @@
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     nf-core/sarek Nextflow base config file
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     A 'blank slate' config file, appropriate for general use on most high performance
     compute environments. Assumes that all software is installed and available on
     the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.

conf/igenomes.config

@@ -1,7 +1,7 @@
 /*
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Nextflow config file for iGenomes paths
-========================================================================================
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines reference genomes using iGenome paths.
     Can be used by any config that customises the base path using:
         $params.igenomes_base / --igenomes_base