Merge pull request #940 from d4straub/fix-conda-2.16.0

Fix conda for upcoming release 2.16.0

Author: d4straub

.github/actions/nf-test/action.yml

@@ -53,7 +53,7 @@ runs:
         auto-update-conda: true
         conda-solver: libmamba
         channels: conda-forge
-        channel-priority: strict
+        channel-priority: flexible # 'strict' would be preferable but 'flexible' is required for QIIME2 2024.10 conda yml file
         conda-remove-defaults: true
 
     - name: Run nf-test

.github/workflows/nf-test.yml

@@ -79,7 +79,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.04.8"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

CHANGELOG.md

@@ -3,30 +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 2.16.0 - 2025-12-19
+## nf-core/ampliseq version 2.16.0 - 2026-01-14
 
 ### `Added`
 
 ### `Changed`
 
-[#928](https://github.com/nf-core/ampliseq/pull/928) - Resource allocations were reduced for most smaller processes.
-[#931](https://github.com/nf-core/ampliseq/pull/931) - For `--dada_ref_taxonomy`, replace `sbdi-gtdb=R10-RS226-1` with updated database `sbdi-gtdb=R10-RS226-2` (see https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/10)
+- [#928](https://github.com/nf-core/ampliseq/pull/928) - Resource allocations were reduced for most smaller processes.
+- [#931](https://github.com/nf-core/ampliseq/pull/931) - For `--dada_ref_taxonomy`, replace `sbdi-gtdb=R10-RS226-1` with updated database `sbdi-gtdb=R10-RS226-2` (see https://figshare.scilifelab.se/articles/dataset/SBDI_Sativa_curated_16S_GTDB_database/14869077/10)
 
 ### `Fixed`
 
-[#926](https://github.com/nf-core/ampliseq/pull/926),[932](https://github.com/nf-core/ampliseq/pull/932) - Template update for nf-core/tools version 3.5.1
-[#929](https://github.com/nf-core/ampliseq/pull/929),[#935](https://github.com/nf-core/ampliseq/pull/935) - A bug in a dependency of MultiQC can lead (rarely) to plot generation being omitted, without warning. In that case, the subsequent pipeline summary report failed previously, now it gracefully handles that issue.
+- [#926](https://github.com/nf-core/ampliseq/pull/926),[932](https://github.com/nf-core/ampliseq/pull/932) - Template update for nf-core/tools version 3.5.1
+- [#929](https://github.com/nf-core/ampliseq/pull/929),[#935](https://github.com/nf-core/ampliseq/pull/935) - A bug in a dependency of MultiQC can lead (rarely) to plot generation being omitted, without warning. In that case, the subsequent pipeline summary report failed previously, now it gracefully handles that issue.
 
 ### `Dependencies`
 
-- [#936](https://github.com/nf-core/ampliseq/pull/936) - Updated some software versions
+- [#936](https://github.com/nf-core/ampliseq/pull/936),[#940](https://github.com/nf-core/ampliseq/pull/940) - Updated some software versions
 
-| software | previously | now    |
-| -------- | ---------- | ------ |
-| Cutadapt | 4.6        | 5.2    |
-| DADA2    | 1.30.0     | 1.34.0 |
-| Phyloseq | 1.46.0     | 1.50.0 |
-| MultiQC  | 1.29       | 1.33   |
+| software | previously | now       |
+| -------- | ---------- | --------- |
+| nextflow | >=25.04.0  | >=25.04.8 |
+| Cutadapt | 4.6        | 5.2       |
+| DADA2    | 1.30.0     | 1.34.0    |
+| Phyloseq | 1.46.0     | 1.50.0    |
+| MultiQC  | 1.29       | 1.33      |
 
 ### `Removed`
 

README.md

@@ -11,7 +11,7 @@
 
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841)[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![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/)

modules/local/cutadapt_summary_merge.nf

@@ -2,7 +2,7 @@ process CUTADAPT_SUMMARY_MERGE {
     tag "${files}"
     label 'process_single'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"

modules/local/dada2_addspecies.nf

@@ -4,7 +4,7 @@ process DADA2_ADDSPECIES {
     label 'process_medium_memory'
     label 'process_long'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"

modules/local/dada2_denoising.nf

@@ -4,7 +4,7 @@ process DADA2_DENOISING {
     label 'process_long'
     label 'error_retry'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"

modules/local/dada2_err.nf

@@ -2,7 +2,7 @@ process DADA2_ERR {
     tag "$meta.run"
     label 'process_medium'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"

modules/local/dada2_filtntrim.nf

@@ -2,7 +2,7 @@ process DADA2_FILTNTRIM {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"

modules/local/dada2_quality.nf

@@ -2,7 +2,7 @@ process DADA2_QUALITY {
     tag "$meta"
     label 'process_low'
 
-    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
+    conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
         'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"