diff --git a/.github/actions/nf-test/action.yml b/.github/actions/nf-test/action.yml index 3b9724c7..5c9c5426 100644 --- a/.github/actions/nf-test/action.yml +++ b/.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 diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index cf815a15..1245101a 100644 --- a/.github/workflows/nf-test.yml +++ b/.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 diff --git a/CHANGELOG.md b/CHANGELOG.md index 4ddc0804..4b23d430 100644 --- a/CHANGELOG.md +++ b/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` diff --git a/README.md b/README.md index 760c1d0c..b39fea66 100644 --- a/README.md +++ b/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/) diff --git a/modules/local/cutadapt_summary_merge.nf b/modules/local/cutadapt_summary_merge.nf index eb7a81b2..16b32f98 100644 --- a/modules/local/cutadapt_summary_merge.nf +++ b/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' }" diff --git a/modules/local/dada2_addspecies.nf b/modules/local/dada2_addspecies.nf index a89a0550..0af7daf3 100644 --- a/modules/local/dada2_addspecies.nf +++ b/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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' : 'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }" diff --git a/modules/local/dada2_denoising.nf b/modules/local/dada2_denoising.nf index 43f91263..b047a9df 100644 --- a/modules/local/dada2_denoising.nf +++ b/modules/local/dada2_denoising.nf @@ -4,7 +4,7 @@ process DADA2_DENOISING { label 'process_long' label 'error_retry' - conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3" + conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2" container "${ 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' }" diff --git a/modules/local/dada2_err.nf b/modules/local/dada2_err.nf index 37d21df6..b45c8214 100644 --- a/modules/local/dada2_err.nf +++ b/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' }" diff --git a/modules/local/dada2_filtntrim.nf b/modules/local/dada2_filtntrim.nf index 385c35c1..b761e9aa 100644 --- a/modules/local/dada2_filtntrim.nf +++ b/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' }" diff --git a/modules/local/dada2_quality.nf b/modules/local/dada2_quality.nf index f28145b1..9d0415fe 100644 --- a/modules/local/dada2_quality.nf +++ b/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' }" diff --git a/modules/local/dada2_rmchimera.nf b/modules/local/dada2_rmchimera.nf index 0f2b57f6..df74b149 100644 --- a/modules/local/dada2_rmchimera.nf +++ b/modules/local/dada2_rmchimera.nf @@ -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' }" diff --git a/modules/local/dada2_stats.nf b/modules/local/dada2_stats.nf index 90b16b86..deed2513 100644 --- a/modules/local/dada2_stats.nf +++ b/modules/local/dada2_stats.nf @@ -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' }" diff --git a/modules/local/dada2_taxonomy.nf b/modules/local/dada2_taxonomy.nf index 017a06e2..091265d7 100644 --- a/modules/local/dada2_taxonomy.nf +++ b/modules/local/dada2_taxonomy.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' : 'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }" diff --git a/modules/local/format_pplacetax.nf b/modules/local/format_pplacetax.nf index 633c684d..7d3adb91 100644 --- a/modules/local/format_pplacetax.nf +++ b/modules/local/format_pplacetax.nf @@ -2,7 +2,7 @@ process FORMAT_PPLACETAX { tag "${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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' : 'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }" diff --git a/modules/local/merge_stats.nf b/modules/local/merge_stats.nf index b9cbddd2..c3e98f6c 100644 --- a/modules/local/merge_stats.nf +++ b/modules/local/merge_stats.nf @@ -1,7 +1,7 @@ process MERGE_STATS { label 'process_single' - conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3" + conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3 conda-forge::tbb=2020.2" container "${ 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' }" diff --git a/modules/local/metadata_all.nf b/modules/local/metadata_all.nf index 9770be66..ee85f700 100644 --- a/modules/local/metadata_all.nf +++ b/modules/local/metadata_all.nf @@ -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' }" diff --git a/modules/local/metadata_pairwise.nf b/modules/local/metadata_pairwise.nf index 82b82adf..ed0cba2a 100644 --- a/modules/local/metadata_pairwise.nf +++ b/modules/local/metadata_pairwise.nf @@ -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' }" diff --git a/modules/local/novaseq_err.nf b/modules/local/novaseq_err.nf index ec94680f..d47901ef 100644 --- a/modules/local/novaseq_err.nf +++ b/modules/local/novaseq_err.nf @@ -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' }" diff --git a/nextflow.config b/nextflow.config index 09f10d60..78effd1a 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 8c861d5f..4b3e8c2b 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "Stable", "datePublished": "2025-12-18T14:45:34+00:00", - "description": "

\n \n \n \"nf-core/ampliseq\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/ampliseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/ampliseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ampliseq/results)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![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)\n\n[![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/)\n[![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)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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)\n\n[![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 Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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)\n\n## Introduction\n\n**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Multiple region analysis such as 5R is implemented. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.\n\nA video about relevance, usage and output of the pipeline (version 2.1.0; 26th Oct. 2021) can also be found in [YouTube](https://youtu.be/a0VOEeAvETs) and [billibilli](https://www.bilibili.com/video/BV1B44y1e7MM), the slides are deposited at [figshare](https://doi.org/10.6084/m9.figshare.16871008.v1).\n\n

\n \"nf-core/ampliseq\n

\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/ampliseq/results).\n\n## Pipeline summary\n\nBy default, the pipeline currently performs the following:\n\n- Sequencing quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n- Trimming of reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200))\n- Infer Amplicon Sequence Variants (ASVs) ([DADA2](https://doi.org/10.1038/nmeth.3869))\n- Optional post-clustering with [VSEARCH](https://github.com/torognes/vsearch)\n- Predict whether ASVs are ribosomal RNA sequences ([Barrnap](https://github.com/tseemann/barrnap))\n- Phylogenetic placement ([EPA-NG](https://github.com/Pbdas/epa-ng))\n- 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)\n- 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))\n- Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html) and [TreeSE](https://doi.org/10.12688/f1000research.26669.2))\n- Pipeline QC summaries ([MultiQC](https://multiqc.info/))\n- Pipeline summary report ([R Markdown](https://github.com/rstudio/rmarkdown))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, you need to know whether the sequencing files at hand are expected to contain primer sequences (usually yes) and if yes, what primer sequences. In the example below, the paired end sequencing data was produced with 515f (GTGYCAGCMGCCGCGGTAA) and 806r (GGACTACNVGGGTWTCTAAT) primers of the V4 region of the 16S rRNA gene. Please note, that those sequences should not contain any sequencing adapter sequences, only the sequence that matches the biological amplicon.\n\nNext, the data needs to be organized in a folder, here `data`, or detailed in a samplesheet (see [input documentation](https://nf-co.re/ampliseq/usage#input-specifications)).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/ampliseq \\\n -profile \\\n --input \"data\" \\\n --FW_primer \"GTGYCAGCMGCCGCGGTAA\" \\\n --RV_primer \"GGACTACNVGGGTWTCTAAT\" \\\n --outdir \n```\n\n> [!NOTE]\n> Adding metadata will considerably increase the output, see [metadata documentation](https://nf-co.re/ampliseq/usage#metadata).\n\n> [!TIP]\n> 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.\n\n> [!WARNING]\n> 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/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor 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).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/ampliseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/ampliseq/output).\n\n## Credits\n\nnf-core/ampliseq was originally written by Daniel Straub ([@d4straub](https://github.com/d4straub)) and Alexander Peltzer ([@apeltzer](https://github.com/apeltzer)) for use at the [Quantitative Biology Center (QBiC)](https://www.info.qbic.uni-tuebingen.de/) and [Microbial Ecology, Center for Applied Geosciences](http://www.uni-tuebingen.de/de/104325), part of Eberhard Karls Universit\u00e4t T\u00fcbingen (Germany). Daniel Lundin [@erikrikarddaniel](https://github.com/erikrikarddaniel) ([Linnaeus University, Sweden](https://lnu.se/)) joined before pipeline release 2.0.0 and helped to improve the pipeline considerably.\n\nWe thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order):\n\n[Adam Bennett](https://github.com/a4000), [Diego Brambilla](https://github.com/DiegoBrambilla), [Emelie Nilsson](https://github.com/emnilsson), [Jeanette T\u00e5ngrot](https://github.com/jtangrot), [Lokeshwaran Manoharan](https://github.com/lokeshbio), [Marissa Dubbelaar](https://github.com/marissaDubbelaar), [Sabrina Krakau](https://github.com/skrakau), [Sam Minot](https://github.com/sminot), [Till Englert](https://github.com/tillenglert)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#ampliseq` channel](https://nfcore.slack.com/channels/ampliseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use `nf-core/ampliseq` for your analysis, please cite the `ampliseq` article as follows:\n\n> **Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline**\n>\n> Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst\n>\n> _Frontiers in Microbiology_ 2020, 11:2652 [doi: 10.3389/fmicb.2020.550420](https://doi.org/10.3389/fmicb.2020.550420).\n\nYou can cite the `nf-core/ampliseq` zenodo record for a specific version using the following [doi: 10.5281/zenodo.1493841](https://zenodo.org/badge/latestdoi/150448201)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "

\n \n \n \"nf-core/ampliseq\"\n \n

\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/nf-core/ampliseq)\n[![GitHub Actions CI Status](https://github.com/nf-core/ampliseq/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ampliseq/results)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![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)\n\n[![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/)\n[![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)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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)\n\n[![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 Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![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)\n\n## Introduction\n\n**nfcore/ampliseq** is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S. Phylogenetic placement is also possible. Multiple region analysis such as 5R is implemented. Supported is paired-end Illumina or single-end Illumina, PacBio and IonTorrent data. Default is the analysis of 16S rRNA gene amplicons sequenced paired-end with Illumina.\n\nA video about relevance, usage and output of the pipeline (version 2.1.0; 26th Oct. 2021) can also be found in [YouTube](https://youtu.be/a0VOEeAvETs) and [billibilli](https://www.bilibili.com/video/BV1B44y1e7MM), the slides are deposited at [figshare](https://doi.org/10.6084/m9.figshare.16871008.v1).\n\n

\n \"nf-core/ampliseq\n

\n\nOn release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/ampliseq/results).\n\n## Pipeline summary\n\nBy default, the pipeline currently performs the following:\n\n- Sequencing quality control ([FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n- Trimming of reads ([Cutadapt](https://journal.embnet.org/index.php/embnetjournal/article/view/200))\n- Infer Amplicon Sequence Variants (ASVs) ([DADA2](https://doi.org/10.1038/nmeth.3869))\n- Optional post-clustering with [VSEARCH](https://github.com/torognes/vsearch)\n- Predict whether ASVs are ribosomal RNA sequences ([Barrnap](https://github.com/tseemann/barrnap))\n- Phylogenetic placement ([EPA-NG](https://github.com/Pbdas/epa-ng))\n- 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)\n- 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))\n- Creates phyloseq R objects ([Phyloseq](https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html) and [TreeSE](https://doi.org/10.12688/f1000research.26669.2))\n- Pipeline QC summaries ([MultiQC](https://multiqc.info/))\n- Pipeline summary report ([R Markdown](https://github.com/rstudio/rmarkdown))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, you need to know whether the sequencing files at hand are expected to contain primer sequences (usually yes) and if yes, what primer sequences. In the example below, the paired end sequencing data was produced with 515f (GTGYCAGCMGCCGCGGTAA) and 806r (GGACTACNVGGGTWTCTAAT) primers of the V4 region of the 16S rRNA gene. Please note, that those sequences should not contain any sequencing adapter sequences, only the sequence that matches the biological amplicon.\n\nNext, the data needs to be organized in a folder, here `data`, or detailed in a samplesheet (see [input documentation](https://nf-co.re/ampliseq/usage#input-specifications)).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/ampliseq \\\n -profile \\\n --input \"data\" \\\n --FW_primer \"GTGYCAGCMGCCGCGGTAA\" \\\n --RV_primer \"GGACTACNVGGGTWTCTAAT\" \\\n --outdir \n```\n\n> [!NOTE]\n> Adding metadata will considerably increase the output, see [metadata documentation](https://nf-co.re/ampliseq/usage#metadata).\n\n> [!TIP]\n> 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.\n\n> [!WARNING]\n> 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/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor 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).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/ampliseq/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/ampliseq/output).\n\n## Credits\n\nnf-core/ampliseq was originally written by Daniel Straub ([@d4straub](https://github.com/d4straub)) and Alexander Peltzer ([@apeltzer](https://github.com/apeltzer)) for use at the [Quantitative Biology Center (QBiC)](https://www.info.qbic.uni-tuebingen.de/) and [Microbial Ecology, Center for Applied Geosciences](http://www.uni-tuebingen.de/de/104325), part of Eberhard Karls Universit\u00e4t T\u00fcbingen (Germany). Daniel Lundin [@erikrikarddaniel](https://github.com/erikrikarddaniel) ([Linnaeus University, Sweden](https://lnu.se/)) joined before pipeline release 2.0.0 and helped to improve the pipeline considerably.\n\nWe thank the following people for their extensive assistance in the development of this pipeline (in alphabetical order):\n\n[Adam Bennett](https://github.com/a4000), [Diego Brambilla](https://github.com/DiegoBrambilla), [Emelie Nilsson](https://github.com/emnilsson), [Jeanette T\u00e5ngrot](https://github.com/jtangrot), [Lokeshwaran Manoharan](https://github.com/lokeshbio), [Marissa Dubbelaar](https://github.com/marissaDubbelaar), [Sabrina Krakau](https://github.com/skrakau), [Sam Minot](https://github.com/sminot), [Till Englert](https://github.com/tillenglert)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#ampliseq` channel](https://nfcore.slack.com/channels/ampliseq) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use `nf-core/ampliseq` for your analysis, please cite the `ampliseq` article as follows:\n\n> **Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline**\n>\n> Daniel Straub, Nia Blackwell, Adrian Langarica-Fuentes, Alexander Peltzer, Sven Nahnsen, Sara Kleindienst\n>\n> _Frontiers in Microbiology_ 2020, 11:2652 [doi: 10.3389/fmicb.2020.550420](https://doi.org/10.3389/fmicb.2020.550420).\n\nYou can cite the `nf-core/ampliseq` zenodo record for a specific version using the following [doi: 10.5281/zenodo.1493841](https://zenodo.org/badge/latestdoi/150448201)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -213,7 +213,7 @@ "url": { "@id": "https://www.nextflow.io/" }, - "version": "!>=25.04.0" + "version": "!>=25.04.8" }, { "@id": "#414b9990-2f05-4527-a72a-bc79dbf68dfb",