Dev -> Master for 2.2 release

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,42 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+
+  - type: markdown
+    attributes:
+      value: |
+        Hi there!
+
+        Thanks for telling us about a problem with the nf-core/tools package.
+
+  - 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 and output from your terminal.
+      render: console
+      placeholder: |
+        $ nf-core lint ...
+
+        Some output where something broke
+
+  - 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)_
+        * OS _(eg. CentOS Linux, macOS, Linux Mint)_
+        * Version of nf-core/tools _(eg. 1.1, 1.5, 1.8.2)_
+        * Python version _(eg. 3.7, 3.8)_

.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 nf-core/tools
+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/create-lint-wf.yml

@@ -1,12 +1,15 @@
 name: Create a pipeline and lint it
 on: [push, pull_request]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
   MakeTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: ["NXF_VER=21.10.3", "NXF_EDGE=1"]
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -27,6 +30,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
 
       - name: nf-core create
         run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface"

.github/workflows/create-test-wf.yml

@@ -1,12 +1,17 @@
 name: Create a pipeline and test it
 on: [push, pull_request]
 
-# Uncomment if we need an edge release of Nextflow again
-# env: NXF_EDGE: 1
-
 jobs:
   RunTestWorkflow:
     runs-on: ubuntu-latest
+    env:
+      NXF_ANSI_LOG: false
+    strategy:
+      matrix:
+        # Nextflow versions: check pipeline minimum and latest edge version
+        nxf_ver: 
+          - "NXF_VER=21.10.3"
+          # - "NXF_EDGE=1"
     steps:
       - uses: actions/checkout@v2
         name: Check out source-code repository
@@ -27,6 +32,8 @@ jobs:
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
+          export ${{ matrix.nxf_ver }}
+          nextflow self-update
 
       - name: Run nf-core/tools
         run: |

.github/workflows/push_dockerhub_dev.yml

@@ -3,31 +3,28 @@ name: nf-core Docker push (dev)
 # Runs on nf-core repo releases and push event to 'dev' branch (PR merges)
 on:
   push:
-    branches:
-      - dev
+    branches: [dev]
 
 jobs:
   push_dockerhub:
     name: Push new Docker image to Docker Hub (dev)
     runs-on: ubuntu-latest
     # Only run for the nf-core repo, for releases and merged PRs
-    if: ${{ github.repository == 'nf-core/tools'}}
+    if: ${{ github.repository == 'nf-core/tools' }}
     env:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
     strategy:
-      matrix:
-        image: [base, tools]
       fail-fast: false
     steps:
-      - name: Check out tools code
+      - name: Check out code
         uses: actions/checkout@v2
 
       - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/${{ matrix.image }}:dev -f ${{ matrix.image }}.Dockerfile
+        run: docker build --no-cache . -t nfcore/tools:dev
 
       - name: Push Docker image to DockerHub (dev)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/${{ matrix.image }}:dev
+          docker push nfcore/tools:dev
 

.github/workflows/push_dockerhub_release.yml

@@ -15,19 +15,17 @@ jobs:
       DOCKERHUB_USERNAME: ${{ secrets.DOCKERHUB_USERNAME }}
       DOCKERHUB_PASS: ${{ secrets.DOCKERHUB_PASS }}
     strategy:
-      matrix:
-        image: [base, tools]
       fail-fast: false
     steps:
       - name: Check out code
         uses: actions/checkout@v2
 
       - name: Build new docker image
-        run: docker build --no-cache . -t nfcore/${{ matrix.image }}:latest -f ${{ matrix.image }}.Dockerfile
+        run: docker build --no-cache . -t nfcore/tools:latest
 
       - name: Push Docker image to DockerHub (release)
         run: |
           echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-          docker push nfcore/${{ matrix.image }}:latest
-          docker tag nfcore/${{ matrix.image }}:latest nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}
-          docker push nfcore/${{ matrix.image }}:${{ github.event.release.tag_name }}
+          docker push nfcore/tools:latest
+          docker tag nfcore/tools:latest nfcore/tools:${{ github.event.release.tag_name }}
+          docker push nfcore/tools:${{ github.event.release.tag_name }}

.github/workflows/pytest.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
 
     steps:
       - uses: actions/checkout@v2

.github/workflows/python-lint.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Check code lints with Black
-        uses: jpetrucciani/black-check@master
+        uses: psf/black@stable
 
       # If the above check failed, post a comment on the PR explaining the failure
       - name: Post PR comment

CHANGELOG.md

@@ -1,5 +1,59 @@
 # nf-core/tools: Changelog
 
+## [v2.2 - Lead Liger](https://github.com/nf-core/tools/releases/tag/2.2) - [2021-12-14]
+
+### Template
+
+* Update repo logos to utilize [GitHub's `#gh-light/dark-mode-only`](https://docs.github.com/en/github/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax#specifying-the-theme-an-image-is-shown-to), to switch between logos optimized for light or dark themes. The old repo logos have to be removed (in `docs/images` and `assets/`).
+* Deal with authentication with private repositories
+* Bump minimun Nextflow version to 21.10.3
+* Convert pipeline template to updated Nextflow DSL2 syntax
+* Solve circular import when importing `nf_core.modules.lint`
+* Disable cache in `nf_core.utils.fetch_wf_config` while performing `test_wf_use_local_configs`.
+* Modify software version channel handling to support multiple software version emissions (e.g. from mulled containers), and multiple software versions.
+* Update `dumpsoftwareversion` module to correctly report versions with trailing zeros.
+* Remove `params.hostnames` from the pipeline template ([#1304](https://github.com/nf-core/tools/issues/1304))
+* Update `.gitattributes` to mark installed modules and subworkflows as `linguist-generated` ([#1311](https://github.com/nf-core/tools/issues/1311))
+* Adding support for [Julia](https://julialang.org) package environments to `nextflow.config`([#1317](https://github.com/nf-core/tools/pull/1317))
+* New YAML issue templates for pipeline bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
+* Update AWS test GitHub Actions to use v2 of [nf-core/tower-action](https://github.com/nf-core/tower-action)
+* Post linting comment even when `linting.yml` fails
+* Update `CONTRIBUTION.md` bullets to remove points related to `scrape_software_versions.py`
+* Update AWS test to set Nextflow version to 21.10.3
+
+### General
+
+* Made lint check for parameters defaults stricter [[#992](https://github.com/nf-core/tools/issues/992)]
+    * Default values in `nextflow.config` must match the defaults given in the schema (anything with `{` in, or in `main.nf` is ignored)
+    * Defaults in `nextflow.config` must now match the variable _type_ specified in the schema
+    * If you want the parameter to not have a default value, use `null`
+    * Strings set to `false` or an empty string in `nextflow.config` will now fail linting
+* Bump minimun Nextflow version to 21.10.3
+* Changed `questionary` `ask()` to `unsafe_ask()` to not catch `KeyboardInterupts` ([#1237](https://github.com/nf-core/tools/issues/1237))
+* Fixed bug in `nf-core launch` due to revisions specified with `-r` not being added to nextflow command. ([#1246](https://github.com/nf-core/tools/issues/1246))
+* Update regex in `readme` test of `nf-core lint` to agree with the pipeline template ([#1260](https://github.com/nf-core/tools/issues/1260))
+* Update 'fix' message in `nf-core lint` to conform to the current command line options. ([#1259](https://github.com/nf-core/tools/issues/1259))
+* Fixed bug in `nf-core list` when `NXF_HOME` is set
+* Run CI test used to create and lint/run the pipeline template with minimum and latest edge release of NF ([#1304](https://github.com/nf-core/tools/issues/1304))
+* New YAML issue templates for tools bug reports and feature requests, with a much richer interface ([#1165](https://github.com/nf-core/tools/pull/1165))
+* Handle synax errors in Nextflow config nicely when running `nf-core schema build` ([#1267](https://github.com/nf-core/tools/pull/1267))
+* Erase temporary files and folders while performing Python tests (pytest)
+* Remove base `Dockerfile` used for DSL1 pipeline container builds
+* Run tests with Python 3.10
+
+### Modules
+
+* Fixed typo in `module_utils.py`.
+* Fixed failing lint test when process section was missing from module. Also added the local failing tests to the warned section of the output table. ([#1235](https://github.com/nf-core/tools/issues/1235))
+* Added `--diff` flag to `nf-core modules update` which shows the diff between the installed files and the versions
+* Update `nf-core modules create` help texts which were not changed with the introduction of the `--dir` flag
+* Check if README is from modules repo
+* Update module template to DSL2 v2.0 (remove `functions.nf` from modules template and updating `main.nf` ([#1289](https://github.com/nf-core/tools/pull/))
+* Substitute get process/module name custom functions in module `main.nf` using template replacement ([#1284](https://github.com/nf-core/tools/issues/1284))
+* Linting now fails instead of warning if a local copy of a module does not match the remote ([#1313](https://github.com/nf-core/tools/issues/1313))
+* Check test YML file for md5sums corresponding to empty files ([#1302](https://github.com/nf-core/tools/issues/1302))
+* Exit with an error if empty files are found when generating the test YAML file ([#1302](https://github.com/nf-core/tools/issues/1302))
+
 ## [v2.1 - Zinc Zebra](https://github.com/nf-core/tools/releases/tag/2.1) - [2021-07-27]
 
 ### Template

MANIFEST.in

@@ -1,3 +1,5 @@
 include LICENSE
 include README.md
-recursive-include nf_core *
+graft nf_core/module-template
+graft nf_core/pipeline-template
+include requirements.txt