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Fix conda for upcoming release 2.16.0 #940

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Merged
d4straub merged 4 commits into from
Jan 14, 2026
+33 −32
Merged

Fix conda for upcoming release 2.16.0 #940

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5de1e7f
update minimum nextflow version to 25.04.8
d4straub Jan 8, 2026
4ce5fdf
pinning conda-forge::tbb=2020.2 for DADA2 1.34.0 conda env
d4straub Jan 13, 2026
f365200
for CI tests set channel-priority: flexible
d4straub Jan 13, 2026
648e0f2
update CHANGELOG
d4straub Jan 13, 2026
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2 changes: 1 addition & 1 deletion .github/actions/nf-test/action.yml
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Expand Up @@ -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
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@ebete ebete Jan 13, 2026

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I think this can be set to strict if the QIIME2 environment definition includes the channel for each package (e.g., bioconda::blast==2.17.0)

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@d4straub d4straub Jan 13, 2026

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Thanks! But the QIIME2 conda yml file contains 756 lines, and none of the packages are defined with channels, it comes from the QIIME2 developers with that flaw. I would like to keep it as is for now.

conda-remove-defaults: true

- name: Run nf-test
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2 changes: 1 addition & 1 deletion .github/workflows/nf-test.yml
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Expand Up @@ -79,7 +79,7 @@ jobs:
- isMain: false
profile: "singularity"
NXF_VER:
- "25.04.0"
- "25.04.8"
- "latest-everything"
env:
NXF_ANSI_LOG: false
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25 changes: 13 additions & 12 deletions CHANGELOG.md
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Expand Up @@ -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`

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -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/)
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2 changes: 1 addition & 1 deletion modules/local/cutadapt_summary_merge.nf
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Expand Up @@ -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' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_addspecies.nf
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Expand Up @@ -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' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_denoising.nf
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Expand Up @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_err.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_ERR {
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_filtntrim.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_FILTNTRIM {
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_quality.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_QUALITY {
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_rmchimera.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_RMCHIMERA {
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_stats.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_STATS {
tag "$meta.run"
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/dada2_taxonomy.nf
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Expand Up @@ -2,7 +2,7 @@ process DADA2_TAXONOMY {
tag "${fasta},${database}"
label 'process_high'

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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/format_pplacetax.nf
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Expand Up @@ -2,7 +2,7 @@ process FORMAT_PPLACETAX {
tag "${tax.baseName}"
label 'process_high'

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' }"
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2 changes: 1 addition & 1 deletion modules/local/merge_stats.nf
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@@ -1,7 +1,7 @@
process MERGE_STATS {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/metadata_all.nf
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Expand Up @@ -2,7 +2,7 @@ process METADATA_ALL {
tag "$metadata"
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/metadata_pairwise.nf
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Expand Up @@ -2,7 +2,7 @@ process METADATA_PAIRWISE {
tag "$metadata"
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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2 changes: 1 addition & 1 deletion modules/local/novaseq_err.nf
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Expand Up @@ -2,7 +2,7 @@ process NOVASEQ_ERR {
tag "$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' }"
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -414,7 +414,7 @@ manifest {
description = """Amplicon sequencing analysis workflow using DADA2 and QIIME2"""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.04.0'
nextflowVersion = '!>=25.04.8'
version = '2.16.0'
doi = '10.5281/zenodo.1493841,10.3389/fmicb.2020.550420'
}
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