Template update for nf-core/tools version 2.2

.gitattributes

@@ -1 +1,3 @@
 *.config linguist-language=nextflow
+modules/nf-core/** linguist-generated
+subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -68,16 +68,13 @@ If you wish to contribute a new step, please use the following coding standards:
 1. Define the corresponding input channel into your new process from the expected previous process channel
 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`).
-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`.
-9. Do local tests that the new code works properly and as expected.
-10. Add a new test command in `.github/workflow/ci.yml`.
-11. If applicable add a [MultiQC](https://https://multiqc.info/) module.
-12. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, name clean up, General Statistics Table column order, and module figures are in the right order.
-13. Optional: Add any descriptions of MultiQC report sections and output files to `docs/output.md`.
+4. Add any new parameters to `nextflow.config` with a default (see below).
+5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool).
+6. Add sanity checks and validation for all relevant parameters.
+7. Perform local tests to validate that the new code works as expected.
+8. If applicable, add a new test command in `.github/workflow/ci.yml`.
+9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
 
@@ -102,27 +99,6 @@ Please use the following naming schemes, to make it easy to understand what is g
 
 If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]`
 
-### Software version reporting
-
-If you add a new tool to the pipeline, please ensure you add the information of the tool to the `get_software_version` process.
-
-Add to the script block of the process, something like the following:
-
-```bash
-<YOUR_TOOL> --version &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-or
-
-```bash
-<YOUR_TOOL> --help | head -n 1 &> v_<YOUR_TOOL>.txt 2>&1 || true
-```
-
-You then need to edit the script `bin/scrape_software_versions.py` to:
-
-1. Add a Python regex for your tool's `--version` output (as in stored in the `v_<YOUR_TOOL>.txt` file), to ensure the version is reported as a `v` and the version number e.g. `v2.1.1`
-2. Add a HTML entry to the `OrderedDict` for formatting in MultiQC.
-
 ### Images and figures
 
 For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,52 @@
+
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Before you post this issue, please check the documentation:
+
+        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
+        - [nf-core/cutandrun pipeline documentation](https://nf-co.re/cutandrun/usage)
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of the bug
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: command_used
+    attributes:
+      label: Command used and terminal output
+      description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal.
+      render: console
+      placeholder: |
+        $ nextflow run ...
+
+        Some output where something broke
+
+  - type: textarea
+    id: files
+    attributes:
+      label: Relevant files
+      description: |
+        Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed.
+        Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files.
+
+  - type: textarea
+    id: system
+    attributes:
+      label: System information
+      description: |
+        * Nextflow version _(eg. 21.10.3)_
+        * Hardware _(eg. HPC, Desktop, Cloud)_
+        * Executor _(eg. slurm, local, awsbatch)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/cutandrun _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -1,4 +1,3 @@
-blank_issues_enabled: false
 contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Suggest an idea for the nf-core/cutandrun pipeline
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/workflows/awsfulltest.yml

@@ -14,14 +14,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
+        uses: nf-core/tower-action@v2
         # 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
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
@@ -30,5 +30,5 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
             }
-          profiles: '[ "test_full", "aws_tower" ]'
-
+          profiles: test_full,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'

.github/workflows/awstest.yml

@@ -11,18 +11,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@master
+        uses: nf-core/tower-action@v2
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
-          bearer_token: ${{ secrets.TOWER_BEARER_TOKEN }}
+          access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           pipeline: ${{ github.repository }}
           revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/cutandrun/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/cutandrun/results-test-${{ github.sha }}"
             }
-          profiles: '[ "test", "aws_tower" ]'
-
+          profiles: test,aws_tower
+          pre_run_script: 'export NXF_VER=21.10.3'

.github/workflows/ci.yml

@@ -8,29 +8,36 @@ on:
   release:
     types: [published]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
+env:
+  NXF_ANSI_LOG: false
+  CAPSULE_LOG: none
 
 jobs:
   test:
     name: Run workflow tests
     # 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/cutandrun') }}
     runs-on: ubuntu-latest
-    env:
-      NXF_VER: ${{ matrix.nxf_ver }}
-      NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and current latest
-        nxf_ver: ['21.04.0', '']
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
       - name: Install Nextflow
         env:
-          CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/

.github/workflows/linting_comment.yml

@@ -15,6 +15,7 @@ jobs:
         uses: dawidd6/action-download-artifact@v2
         with:
           workflow: linting.yml
+          workflow_conclusion: completed
 
       - name: Get PR number
         id: pr_number

CITATIONS.md

@@ -12,7 +12,7 @@
 
 * [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
+* [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
     > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools

README.md

@@ -1,11 +1,11 @@
-# ![nf-core/cutandrun](docs/images/nf-core-cutandrun_logo.png)
+# ![nf-core/cutandrun](docs/images/nf-core-cutandrun_logo_light.png#gh-light-mode-only) ![nf-core/cutandrun](docs/images/nf-core-cutandrun_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+CI%22)
 [![GitHub Actions Linting Status](https://github.com/nf-core/cutandrun/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/cutandrun/actions?query=workflow%3A%22nf-core+linting%22)
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/cutandrun/results)
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -33,18 +33,21 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.04.0`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
     ```console
-    nextflow run nf-core/cutandrun -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
+    nextflow run nf-core/cutandrun -profile test,YOURPROFILE
     ```
 
+    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` then the pipeline will auto-detect this and attempt to download the Singularity images directly as opposed to performing a conversion from Docker images. If you are persistently observing issues downloading Singularity images directly due to timeout or network issues then please use the `--singularity_pull_docker_container` parameter to pull and convert the Docker image instead. Alternatively, it is highly recommended to use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to pre-download all of the required containers before running the pipeline and to set the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options to be able to store and re-use the images from a central location for future pipeline runs.
+    > * 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 `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!

assets/multiqc_config.yaml

@@ -1,7 +1,7 @@
 report_comment: >
     This report has been generated by the <a href="https://github.com/nf-core/cutandrun" target="_blank">nf-core/cutandrun</a>
     analysis pipeline. For information about how to interpret these results, please see the
-    <a href="https://github.com/nf-core/cutandrun" target="_blank">documentation</a>.
+    <a href="https://nf-co.re/cutandrun" target="_blank">documentation</a>.
 report_section_order:
     software_versions:
         order: -1000