Merge pull request #648 from nf-core/dev

Release 2.7.0

Author: d4straub

.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/ampliseq then the best place to ask is on the nf-core Slack [#ampliseq](https://nfcore.slack.com/channels/ampliseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/ampliseq then the best place to ask is on the nf-core Slack [#ampliseq](https://nfcore.slack.com/channels/ampliseq) 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/awsfulltest.yml

@@ -14,18 +14,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/ampliseq/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/ampliseq/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/ampliseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/ampliseq/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -47,6 +47,7 @@ jobs:
           - "test"
           - "test_single"
           - "test_fasta"
+          - "test_failed"
           - "test_multi"
           - "test_reftaxcustom"
           - "test_doubleprimers"

.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/bluesky-post-action@v0.0.2
+        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

CHANGELOG.md

@@ -3,7 +3,56 @@
 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).
 
-## nf-core/ampliseq version 2.6.1 - 2023-06-27
+## nf-core/ampliseq version 2.7.0 - 2023-10-20
+
+### `Added`
+
+- [#558](https://github.com/nf-core/ampliseq/pull/558),[#619](https://github.com/nf-core/ampliseq/pull/619),[#625](https://github.com/nf-core/ampliseq/pull/625),[#632](https://github.com/nf-core/ampliseq/pull/632),[#644](https://github.com/nf-core/ampliseq/pull/644) - Pipeline summary report
+- [#615](https://github.com/nf-core/ampliseq/pull/615) - Phyloseq R object creation
+- [#622](https://github.com/nf-core/ampliseq/pull/622) - ASV post-clustering with Vsearch
+- [#637](https://github.com/nf-core/ampliseq/pull/637) - Taxonomic classification with Kraken2, parameter `--kraken2_ref_taxonomy`, `--kraken2_ref_tax_custom`, `--kraken2_assign_taxlevels`, `--kraken2_confidence`
+- [#639](https://github.com/nf-core/ampliseq/pull/639) - GTDB release 214.1 for taxonomic classification with DADA2, using `--dada_ref_taxonomy gtdb` or `--dada_ref_taxonomy gtdb=R08-RS214`
+- [#641](https://github.com/nf-core/ampliseq/pull/641) - Continue analysis even when individual files fail the filtering threshold, added parameter `--ignore_failed_filtering`
+
+### `Changed`
+
+- [#616](https://github.com/nf-core/ampliseq/pull/616) - When using a sample sheet with `--input` containing forward and reverse reads, specifying `--single_end` will only extract forward reads and treat the data as single ended instead of extracting forward and reverse reads.
+- [#616](https://github.com/nf-core/ampliseq/pull/616) - `--input` was split into three params: (1) `--input` for samplesheet, (2) `--input_fasta` for ASV/OTU fasta input, (3) `--input_folder` direct FASTQ input
+
+| Param updated | Param old | Accepts                                  |
+| ------------- | --------- | ---------------------------------------- |
+| input         | input     | samplesheet, .tsv/.csv/.yml/.yaml        |
+| input_fasta   | input     | ASV/OTU sequences, .fasta                |
+| input_folder  | input     | Folder containing compressed fastq files |
+
+- [#639](https://github.com/nf-core/ampliseq/pull/639) - `--dada_ref_taxonomy gtdb` points towards GTDB release 214.1 instead of GTDB release 207 for taxonomic classification with DADA2
+- [#645](https://github.com/nf-core/ampliseq/pull/645) - Updated documentation, including workflow figure
+
+### `Fixed`
+
+- [#605](https://github.com/nf-core/ampliseq/pull/605) - Make `--sbdiexport` compatible with PR2 version 5.0.0
+- [#614](https://github.com/nf-core/ampliseq/pull/614),[#620](https://github.com/nf-core/ampliseq/pull/620),[#642](https://github.com/nf-core/ampliseq/pull/642) - Template update for nf-core/tools version 2.10
+- [#617](https://github.com/nf-core/ampliseq/pull/617) - Fix database compatibility check for `--sbdiexport`
+- [#628](https://github.com/nf-core/ampliseq/pull/628) - Fix edge case for sample sheet input when using specific combinations of sampleID and forwardReads or reverseReads that will forward one file too much to cutadapt
+- [#630](https://github.com/nf-core/ampliseq/pull/630) - ASV rRNA (barrnap), length, and codon filter now work with ASV fasta file input
+- [#633](https://github.com/nf-core/ampliseq/pull/633) - UNIFRAC in QIIME2_DIVERSITY_CORE is now prevented from using a GPU to avoid errors
+- [#643](https://github.com/nf-core/ampliseq/pull/643) - Fix using `--skip_dada_addspecies` without `--dada_ref_tax_custom_sp` which was broken in 2.6.0 & 2.6.1
+- [#647](https://github.com/nf-core/ampliseq/pull/647) - Update of credits
+
+### `Dependencies`
+
+- [#646](https://github.com/nf-core/ampliseq/pull/646) - Updated dependencies, see below:
+
+| software | previously | now    |
+| -------- | ---------- | ------ |
+| FASTQC   | 0.11.9     | 0.12.1 |
+| DADA2    | 1.22.0     | 1.28.0 |
+| PICRUSt2 | 2.5.0      | 2.5.2  |
+| QIIME2   | 2022.11    | 2023.7 |
+
+### `Removed`
+
+## nf-core/ampliseq version 2.6.1 - 2023-06-28
 
 ### `Fixed`
 

CITATIONS.md

@@ -18,6 +18,8 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
+
 - [Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200/479)
 
   > Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17.1 (2011): pp-10. doi: 10.14806/ej.17.1.200.
@@ -29,7 +31,7 @@
 - [DADA2](https://pubmed.ncbi.nlm.nih.gov/27214047/)
   > Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23. PMID: 27214047; PMCID: PMC4927377.
 
-### Taxonomic classification and database (only one database)
+### Taxonomic classification and databases
 
 - Classification by [QIIME2 classifier](https://pubmed.ncbi.nlm.nih.gov/29773078/)
 
@@ -109,6 +111,10 @@
 
   > Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O’Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, and Helene Wagner. vegan: Community Ecology Package. 2018. R package version 2.5-3.
 
+- [Phyloseq](https://doi.org/10.1371/journal.pone.0061217)
+
+  > McMurdie PJ, Holmes S (2013). “phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data.” PLoS ONE, 8(4), e61217.
+
 ### Non-default tools
 
 - [ITSx](https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12073)
@@ -139,9 +145,14 @@
 
   > Edgar RC. (2016) SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences, BioRxiv, 074161. Preprint.
 
+- [Kraken2](https://pubmed.ncbi.nlm.nih.gov/31779668/)
+
+  > Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0
+
 ### Summarizing software
 
 - [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.
 
 ## Data
@@ -165,5 +176,8 @@
 
 - [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.