Merge pull request #755 from nf-core/dev

Release 2.10.0

.editorconfig

@@ -28,6 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/ampl
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/ampliseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/ampliseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/awsfulltest.yml

@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/ampliseq'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json

.github/workflows/awstest.yml

@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/ampliseq'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json

.github/workflows/ci.yml

@@ -63,27 +63,10 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
-
-      - name: Check out test data
-        uses: actions/checkout@v3
-        with:
-          repository: nf-core/test-datasets
-          ref: ampliseq
-          path: test-datasets/
-          fetch-depth: 1
-
-      - name: Replace remote paths in samplesheets
-        run: |
-          for f in ${{ github.workspace }}/test-datasets/samplesheets/*.tsv; do
-            sed -i "s=https://github.com/nf-core/test-datasets/raw/ampliseq/testdata/=${{ github.workspace }}/test-datasets/=g" $f
-            echo "========== $f ============"
-            cat $f
-            echo "========================================"
-          done;
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

.github/workflows/download_pipeline.yml

@@ -32,9 +32,12 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -73,11 +76,11 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --skip_qiime --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
         if: ${{ job.steps.stub_run_pipeline.status == failure() }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --skip_qiime --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

.github/workflows/linting.yml

@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -31,7 +31,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

.nf-core.yml

@@ -14,3 +14,4 @@ update:
   https://github.com/nf-core/modules.git:
     nf-core:
       mafft: "feb29be775d9e41750180539e9a3bdce801d0609"
+nf_core_version: "2.14.1"

.pre-commit-config.yaml

@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

CHANGELOG.md

@@ -3,6 +3,31 @@
 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 2.10.0 - 2024-06-27
+
+### `Added`
+
+- [#751](https://github.com/nf-core/ampliseq/pull/751) - Added version R08-RS214 of curated GTDB 16S taxonomy: `sbdi-gtdb=R08-RS214-1` or `sbdi-gtdb` as parameter to `--dada_ref_taxonomy`
+- [#752](https://github.com/nf-core/ampliseq/pull/752) - Added version R09-RS220 of GTDB 16S taxonomy: `gtdb=R09-RS220` or `gtdb` as parameter to `--dada_ref_taxonomy`
+- [#753](https://github.com/nf-core/ampliseq/pull/753), [#756](https://github.com/nf-core/ampliseq/pull/756), [#757](https://github.com/nf-core/ampliseq/pull/757) - ANCOM-BC via QIIME2 can be used with `--ancombc`, `--ancombc_formula`, and `--ancombc_formula_reflvl`, plotting can be modified with thresholds `--ancombc_effect_size` and `--ancombc_significance`
+
+### `Changed`
+
+- [#749](https://github.com/nf-core/ampliseq/pull/749) - Create barplot also when no metadata is given
+- [#753](https://github.com/nf-core/ampliseq/pull/753) - ANCOM via QIIME2 is not run anymore by default but on request whith `--ancom`, therefore `--skip_ancom` was removed
+
+### `Fixed`
+
+- [#747](https://github.com/nf-core/ampliseq/pull/747) - Template update for nf-core/tools version 2.14.1
+- [#748](https://github.com/nf-core/ampliseq/pull/748) - Updating misleading error message and documentation
+- [#750](https://github.com/nf-core/ampliseq/pull/750) - Numbers in `overall_summary.tsv` were fixed (sometimes misleading in 2.9.0 for columns "denoised[F/R]", "merged", and "nochim")
+
+### `Dependencies`
+
+### `Removed`
+
+- [#753](https://github.com/nf-core/ampliseq/pull/753) - `--skip_ancom` was removed
+
 ## nf-core/ampliseq version 2.9.0 - 2024-04-03
 
 ### `Added`

CITATIONS.md

@@ -135,6 +135,10 @@
 
   > Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis. 2015 May 29;26:27663. doi: 10.3402/mehd.v26.27663. PMID: 26028277; PMCID: PMC4450248.
 
+- [ANCOM-BC](https://pubmed.ncbi.nlm.nih.gov/32665548/)
+
+  > Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction. Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7. PMID: 32665548; PMCID: PMC7360769.
+
 - [Adonis](https://doi.org/10.1111/j.1442-9993.2001.01070.pp.x) and [VEGAN](https://CRAN.R-project.org/package=vegan)
 
   > Marti J Anderson. A new method for non-parametric multivariate analysis of variance. Austral ecology, 26(1):32–46, 2001.

README.md

@@ -14,7 +14,7 @@
 [![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/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/ampliseq)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/ampliseq)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23ampliseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/ampliseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)[![Watch on YouTube](http://img.shields.io/badge/youtube-ampliseq-FFFF00?labelColor=000000&logo=youtube)](https://youtu.be/a0VOEeAvETs)
 
@@ -44,7 +44,6 @@ By default, the pipeline currently performs the following:
 - Phylogenetic placement ([EPA-NG](https://github.com/Pbdas/epa-ng))
 - Taxonomical classification using DADA2; alternatives are [SINTAX](https://doi.org/10.1101/074161), [Kraken2](https://doi.org/10.1186/s13059-019-1891-0), and [QIIME2](https://www.nature.com/articles/s41587-019-0209-9)
 - Excludes unwanted taxa, produces absolute and relative feature/taxa count tables and plots, plots alpha rarefaction curves, computes alpha and beta diversity indices and plots thereof ([QIIME2](https://www.nature.com/articles/s41587-019-0209-9))
-- Calls differentially abundant taxa ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277))
 - Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html))
 - Pipeline QC summaries ([MultiQC](https://multiqc.info/))
 - Pipeline summary report ([R Markdown](https://github.com/rstudio/rmarkdown))
@@ -73,11 +72,10 @@ nextflow run nf-core/ampliseq \
 > Adding metadata will considerably increase the output, see [metadata documentation](https://nf-co.re/ampliseq/usage#metadata).
 
 > [!TIP]
-> By default the taxonomic assignment will be performed with DADA2 on SILVA database, but there are various tools and databases readily available, see [taxonomic classification documentation](https://nf-co.re/ampliseq/usage#taxonomic-classification).
+> By default the taxonomic assignment will be performed with DADA2 on SILVA database, but there are various tools and databases readily available, see [taxonomic classification documentation](https://nf-co.re/ampliseq/usage#taxonomic-classification). Differential abundance testing with ([ANCOM](https://www.ncbi.nlm.nih.gov/pubmed/26028277)) or ([ANCOM-BC](https://www.ncbi.nlm.nih.gov/pubmed/32665548)) when opting in.
 
 > [!WARNING]
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/ampliseq/usage) and the [parameter documentation](https://nf-co.re/ampliseq/parameters).
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.9.0" target="_blank">nf-core/ampliseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/ampliseq/releases/tag/2.10.0" target="_blank">nf-core/ampliseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/ampliseq/2.9.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/ampliseq/2.10.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-ampliseq-methods-description":
     order: -1000