Merge pull request #135 from nf-core/dev

Dev -> Master for v1.9 release

Author: drpatelh

.devcontainer/devcontainer.json

@@ -0,0 +1,27 @@
+{
+    "name": "nfcore",
+    "image": "nfcore/gitpod:latest",
+    "remoteUser": "gitpod",
+
+    // Configure tool-specific properties.
+    "customizations": {
+        // Configure properties specific to VS Code.
+        "vscode": {
+            // Set *default* container specific settings.json values on container create.
+            "settings": {
+                "python.defaultInterpreterPath": "/opt/conda/bin/python",
+                "python.linting.enabled": true,
+                "python.linting.pylintEnabled": true,
+                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
+                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
+                "python.linting.flake8Path": "/opt/conda/bin/flake8",
+                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
+                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
+                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+            },
+
+            // Add the IDs of extensions you want installed when the container is created.
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
+        }
+    }
+}

.gitattributes

@@ -1,3 +1,4 @@
 *.config linguist-language=nextflow
+*.nf.test linguist-language=nextflow
 modules/nf-core/** linguist-generated
 subworkflows/nf-core/** linguist-generated

.github/CONTRIBUTING.md

@@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
 ### 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 Codespaces
+
+This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
+
+To get started:
+
+- Open the repo in [Codespaces](https://github.com/nf-core/fetchngs/codespaces)
+- Tools installed
+  - nf-core
+  - Nextflow
+
+Devcontainer specs:
+
+- [DevContainer config](.devcontainer/devcontainer.json)
+- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 21.10.3)_
+        * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_

.github/workflows/ci.yml

@@ -11,6 +11,10 @@ on:
 env:
   NXF_ANSI_LOG: false
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Run pipeline with test data
@@ -20,11 +24,11 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "21.10.3"
+          - "22.10.1"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php
@@ -34,9 +34,9 @@ jobs:
         id: prettier_status
         run: |
           if prettier --check ${GITHUB_WORKSPACE}; then
-            echo "::set-output name=result::pass"
+            echo "result=pass" >> $GITHUB_OUTPUT
           else
-            echo "::set-output name=result::fail"
+            echo "result=fail" >> $GITHUB_OUTPUT
           fi
 
       - name: Run 'prettier --write'

.github/workflows/linting.yml

@@ -4,6 +4,8 @@ name: nf-core linting
 # that the code meets the nf-core guidelines.
 on:
   push:
+    branches:
+      - dev
   pull_request:
   release:
     types: [published]
@@ -12,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -25,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -38,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -69,12 +71,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v3
+      - uses: actions/setup-python@v4
         with:
           python-version: "3.7"
           architecture: "x64"
@@ -97,7 +99,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -18,7 +18,7 @@ jobs:
 
       - name: Get PR number
         id: pr_number
-        run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
+        run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
         uses: marocchino/sticky-pull-request-comment@v2

.prettierignore

@@ -1,5 +1,6 @@
 email_template.html
 adaptivecard.json
+slackreport.json
 .nextflow*
 work/
 data/
@@ -8,3 +9,4 @@ results/
 testing/
 testing*
 *.pyc
+bin/

CHANGELOG.md

@@ -3,6 +3,15 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.9](https://github.com/nf-core/fetchngs/releases/tag/1.9)] - 2022-12-21
+
+### Enhancements & fixes
+
+- Bumped minimum Nextflow version from `21.10.3` -> `22.10.1`
+- Updated pipeline template to [nf-core/tools 2.7.2](https://github.com/nf-core/tools/releases/tag/2.7.2)
+- Added support for generating nf-core/atacseq compatible samplesheets
+- Added `--nf_core_rnaseq_strandedness` parameter to specify value for `strandedness` entry added to samplesheet created when using `--nf_core_pipeline rnaseq`. The default is `auto` which can be used with nf-core/rnaseq v3.10 onwards to auto-detect strandedness during the pipeline execution.
+
 ## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
 
 ### Enhancements & fixes

CITATION.cff

@@ -2,7 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](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/)
@@ -55,14 +55,15 @@ This downloads a text file called `SRR_Acc_List.txt` that can be directly provid
 The columns in the auto-created samplesheet can be tailored to be accepted out-of-the-box by selected nf-core pipelines, these currently include:
 
 - [nf-core/rnaseq](https://nf-co.re/rnaseq/usage#samplesheet-input)
+- [nf-core/atacseq](https://nf-co.re/atacseq/usage#samplesheet-input)
 - Ilumina processing mode of [nf-core/viralrecon](https://nf-co.re/viralrecon/usage#illumina-samplesheet-format)
 - [nf-core/taxprofiler](https://nf-co.re/nf-core/taxprofiler)
 
-You can use the `--nf_core_pipeline` parameter to customise this behaviour e.g. `--nf_core_pipeline rnaseq`. More pipelines will be supported in due course as we adopt and standardise samplesheet input across nf-core.
+See [usage docs](https://nf-co.re/fetchngs/1.8/usage#samplesheet-format) for more details.
 
 ## Quick Start
 
-1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=21.10.3`)
+1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`)
 
 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`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 _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_.
 

README.md

@@ -0,0 +1,34 @@
+{
+    "attachments": [
+        {
+            "fallback": "Plain-text summary of the attachment.",
+            "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
+            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
+            "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
+            "fields": [
+                {
+                    "title": "Command used to launch the workflow",
+                    "value": "```${commandLine}```",
+                    "short": false
+                }
+                <%
+                    if (!success) { %>
+                    ,
+                    {
+                        "title": "Full error message",
+                        "value": "```${errorReport}```",
+                        "short": false
+                    },
+                    {
+                        "title": "Pipeline configuration",
+                        "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>",
+                        "short": false
+                    }
+                    <% }
+                %>
+            ],
+            "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})"
+        }
+    ]
+}