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Merge pull request #936 from d4straub/update-dependencies-2.16.0dev
Update dependencies
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‎CHANGELOG.md‎

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@@ -19,6 +19,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Dependencies`
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- [#936](https://github.com/nf-core/ampliseq/pull/936) - Updated some software versions
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| software | previously | now |
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| -------- | ---------- | ------ |
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| Cutadapt | 4.6 | 5.2 |
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| DADA2 | 1.30.0 | 1.34.0 |
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| Phyloseq | 1.46.0 | 1.50.0 |
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| MultiQC | 1.29 | 1.33 |
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### `Removed`
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## nf-core/ampliseq version 2.15.0 - 2025-10-06

‎conf/modules.config‎

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withName: CUTADAPT_TAXONOMY {
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ext.args = { "--discard-untrimmed --minimum-length 1 -g ${meta.fw_primer}...${meta.rv_primer_revcomp}" }
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ext.outformat = "fasta"
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publishDir = [
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path: { "${params.outdir}/cutadapt" },
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mode: params.publish_dir_mode,

‎docs/output.md‎

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@@ -194,6 +194,7 @@ Optionally, ASV sequences can be filtered for rRNA sequences identified by Barrn
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- `barrnap/`
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- `rrna.<kingdom>.gff`: GFF3 output for rRNA matches per kingdom, where kingdom is one of `bac,arc,mito,euk`.
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- `summary.tsv`: Summary of evalues for each ASV and kingdom
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- `result.tsv`: Classification of ASVs into domains based on the lowest evalue, only if `--filter_ssu` is set.
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- `ASV_seqs.ssu.fasta`: Fasta file with filtered ASV sequences, only if `--filter_ssu` is set.
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- `ASV_table.ssu.tsv`: Counts for each filtered ASV sequence, only if `--filter_ssu` is set.
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- `stats.ssu.tsv`: Tracking read numbers through filtering, for each sample, only if `--filter_ssu` is set.

‎modules.json‎

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"nf-core": {
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"cutadapt": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["modules"]
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"git_sha": "624977dfaf562211e68a8a868ca80acc8461f1ac",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/cutadapt/cutadapt.diff"
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},
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"epang/place": {
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"branch": "master",
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "5cb9a8694da0a0e550921636bb60bc8c56445fd7",
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"installed_by": ["modules"]
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},
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"gappa/examineassign": {
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},
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"kraken2/kraken2": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "1a9dc0fd9f8f61099b3c912df1ab97fac72a1f86",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/kraken2/kraken2/kraken2-kraken2.diff"
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},
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
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"git_sha": "9656d955b700a8707c4a67821ab056f8c1095675",
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"installed_by": ["modules"]
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},
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"pigz/uncompress": {
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"branch": "master",
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"git_sha": "4ef7becf6a2bbc8df466885d10b4051d1f318a6a",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/pigz/uncompress/pigz-uncompress.diff"
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},
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"untar": {
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"branch": "master",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
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"installed_by": ["modules"]
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},
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"vsearch/cluster": {
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"branch": "master",
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"git_sha": "f10b2465108305544f708389324480db1b5e9f34",
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"git_sha": "3bc4793d82c7bf7b10d29b1aa49a5ebe10c0cdd9",
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"installed_by": ["modules"]
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},
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"vsearch/sintax": {
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"branch": "master",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
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"installed_by": ["modules"]
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},
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"vsearch/usearchglobal": {
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"branch": "master",
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"git_sha": "087a2003d9709be9cd580b432a799805777794be",
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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"installed_by": ["modules"]
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}
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}

‎modules/local/cutadapt_summary_merge.nf‎

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tag "${files}"
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label 'process_single'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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input:
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val(action)

‎modules/local/dada2_addspecies.nf‎

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label 'process_medium_memory'
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label 'process_long'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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input:
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path(taxtable)

‎modules/local/dada2_denoising.nf‎

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label 'process_long'
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label 'error_retry'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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tuple val(meta), path("filtered/*"), path(errormodel)

‎modules/local/dada2_err.nf‎

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tag "$meta.run"
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label 'process_medium'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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tuple val(meta), path(reads)

‎modules/local/dada2_filtntrim.nf‎

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tag "$meta.id"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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tuple val(meta), path(reads), val(trunclenf_in), val(trunclenr_in)

‎modules/local/dada2_quality.nf‎

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tag "$meta"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.30.0 conda-forge::r-base=4.3.2"
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conda "bioconda::bioconductor-dada2=1.34.0 conda-forge::r-base=4.4.3"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.30.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.30.0--r43hf17093f_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.34.0--r44he5774e6_2' :
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'biocontainers/bioconductor-dada2:1.34.0--r44he5774e6_2' }"
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tuple val(meta), path(reads)

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