Merge pull request #166 from nf-core/dev

Release Candidate 1.10.1

Author: drpatelh

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

.github/CONTRIBUTING.md

@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/fetchngs then the best place to ask is on the nf-core Slack [#fetchngs](https://nfcore.slack.com/channels/fetchngs) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/fetchngs then the best place to ask is on the nf-core Slack [#fetchngs](https://nfcore.slack.com/channels/fetchngs) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 
@@ -116,4 +118,3 @@ To get started:
 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. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

.github/workflows/ci.yml

@@ -1,9 +1,6 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
   release:
     types: [published]
@@ -24,7 +21,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code

.github/workflows/cloud_tests_full.yml

@@ -27,7 +27,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_full"
-          profiles: test_full,public_aws_ecr
+          profiles: test_full
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",

.github/workflows/cloud_tests_small.yml

@@ -25,7 +25,7 @@ jobs:
           compute_env: ${{ secrets.TOWER_CE_AWS_CPU }}
           workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}"
           run_name: "aws_fetchngs_small"
-          profiles: test,public_aws_ecr
+          profiles: test
           parameters: |
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/[email protected]
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

.nf-core.yml

@@ -1,5 +1,11 @@
 repository_type: pipeline
 lint:
+  actions_ci: false
+  files_exist:
+    - .github/workflows/awsfulltest.yml
+    - .github/workflows/awstest.yml
+    - conf/igenomes.config
+    - lib/WorkflowFetchngs.groovy
   files_unchanged:
     - assets/sendmail_template.txt
     - lib/NfcoreTemplate.groovy

CHANGELOG.md

@@ -3,6 +3,38 @@
 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).
 
+## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Harshil Patel](https://github.com/drpatelh)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
+### Enhancements & fixes
+
+- [#173](https://github.com/nf-core/fetchngs/issues/173) - Add compatibility for sralite files
+- [PR #205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
+- [PR #206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
+- [PR #208](https://github.com/nf-core/fetchngs/pull/208) - Template update with nf-core/tools 2.10
+
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `sra-tools` | 2.11.0      | 3.0.8       |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits

CITATIONS.md

@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-- [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.
-
 - [Python](http://www.python.org)
 
 - [Requests](https://docs.python-requests.org/)
@@ -57,5 +53,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.