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Merge pull request #646 from d4straub/update-dependencies
Update dependencies
2 parents e095039 + 5c8c7c4 commit 0227a31

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‎CHANGELOG.md

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@@ -40,6 +40,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Dependencies`
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- [#646](https://github.com/nf-core/ampliseq/pull/646) - Updated dependencies, see below:
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| software | previously | now |
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| -------- | ---------- | ------ |
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| FASTQC | 0.11.9 | 0.12.1 |
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| DADA2 | 1.22.0 | 1.28.0 |
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| PICRUSt2 | 2.5.0 | 2.5.2 |
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| QIIME2 | 2022.11 | 2023.7 |
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### `Removed`
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## nf-core/ampliseq version 2.6.1 - 2023-06-28

‎conf/ref_databases.config

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@@ -242,17 +242,17 @@ params {
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}
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//QIIME2 taxonomic reference databases
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qiime_ref_databases {
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//SILVA for QIIME2 v2021.2, see https://docs.qiime2.org/2021.2/data-resources/#silva-16s-18s-rrna
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//SILVA for QIIME2 v2023.7, see https://docs.qiime2.org/2023.7/data-resources/#silva-16s-18s-rrna
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'silva=138' {
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title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138"
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file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ]
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file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ]
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citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931"
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license = "https://www.arb-silva.de/silva-license-information/"
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fmtscript = "taxref_reformat_qiime_silva138.sh"
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}
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'silva' {
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title = "QIIME2 pre-formatted SILVA dereplicated at 99% similarity - Version 138"
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file = [ "https://data.qiime2.org/2022.11/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2022.11/common/silva-138-99-tax.qza" ]
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file = [ "https://data.qiime2.org/2023.7/common/silva-138-99-seqs.qza", "https://data.qiime2.org/2023.7/common/silva-138-99-tax.qza" ]
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citation = "https://www.arb-silva.de/; Bokulich, N.A., Robeson, M., Dillon, M.R. bokulich-lab/RESCRIPt. Zenodo. http://doi.org/10.5281/zenodo.3891931"
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license = "https://www.arb-silva.de/silva-license-information/"
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fmtscript = "taxref_reformat_qiime_silva138.sh"
@@ -302,7 +302,7 @@ params {
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}
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'greengenes85' {
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title = "Greengenes 16S - Version 13_8 - clustered at 85% similarity - for testing purposes only"
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file = [ "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2022.11/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ]
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file = [ "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otus.fasta", "https://data.qiime2.org/2023.7/tutorials/training-feature-classifiers/85_otu_taxonomy.txt" ]
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citation = "McDonald, D., Price, M., Goodrich, J. et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 6, 610–618 (2012). https://doi.org/10.1038/ismej.2011.139"
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fmtscript = "taxref_reformat_qiime_greengenes85.sh"
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}

‎modules.json

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@@ -7,7 +7,7 @@
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"nf-core": {
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
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"installed_by": ["modules"]
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},
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"cutadapt": {
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
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"git_sha": "c7494026693ba1a7db683e1520816709db3f05a0",
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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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"mafft": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "feb29be775d9e41750180539e9a3bdce801d0609",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
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"installed_by": ["modules"]
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},
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"untar": {
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"nf-core": {
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"fasta_newick_epang_gappa": {
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"branch": "master",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
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"installed_by": ["subworkflows"]
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}
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}

‎modules/local/cutadapt_summary_merge.nf

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@@ -2,10 +2,10 @@ process CUTADAPT_SUMMARY_MERGE {
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tag "${files}"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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val(action)

‎modules/local/dada2_addspecies.nf

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@@ -3,10 +3,10 @@ process DADA2_ADDSPECIES {
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label 'process_high'
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label 'single_cpu'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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path(taxtable)

‎modules/local/dada2_denoising.nf

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@@ -3,10 +3,10 @@ process DADA2_DENOISING {
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label 'process_medium'
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label 'process_long'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path("filtered/*"), path(errormodel)

‎modules/local/dada2_err.nf

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@@ -2,10 +2,10 @@ process DADA2_ERR {
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tag "$meta.run"
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label 'process_medium'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path(reads)

‎modules/local/dada2_filtntrim.nf

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@@ -2,10 +2,10 @@ process DADA2_FILTNTRIM {
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tag "$meta.id"
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label 'process_medium'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path(reads), val(trunclenf), val(trunclenr)

‎modules/local/dada2_merge.nf

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process DADA2_MERGE {
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label 'process_low'
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// https://depot.galaxyproject.org/singularity/bioconductor-dada2=1.28.0--r43hf17093f_0 doesnt contain 'digest', so keep here v1.22.0
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :

‎modules/local/dada2_quality.nf

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@@ -2,10 +2,10 @@ process DADA2_QUALITY {
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tag "$meta"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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tuple val(meta), path(reads)

‎modules/local/dada2_rmchimera.nf

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@@ -2,10 +2,10 @@ process DADA2_RMCHIMERA {
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tag "$meta.run"
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label 'process_medium'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
8-
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path(seqtab)

‎modules/local/dada2_stats.nf

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@@ -2,10 +2,10 @@ process DADA2_STATS {
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tag "$meta.run"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path("filter_and_trim_files/*"), path(denoised), path(mergers), path(seqtab_nochim)

‎modules/local/dada2_taxonomy.nf

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@@ -2,10 +2,10 @@ process DADA2_TAXONOMY {
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tag "${fasta},${database}"
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label 'process_high'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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path(fasta)

‎modules/local/format_pplacetax.nf

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@@ -2,10 +2,10 @@ process FORMAT_PPLACETAX {
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tag "${tax.baseName}"
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label 'process_high'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path(tax)

‎modules/local/merge_stats.nf

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process MERGE_STATS {
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
6+
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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path('file1.tsv')

‎modules/local/metadata_all.nf

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@@ -2,10 +2,10 @@ process METADATA_ALL {
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tag "$metadata"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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path(metadata)

‎modules/local/metadata_pairwise.nf

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Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@ process METADATA_PAIRWISE {
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tag "$metadata"
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label 'process_low'
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conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
8-
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
7+
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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path(metadata)

‎modules/local/novaseq_err.nf

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@@ -2,10 +2,10 @@ process NOVASEQ_ERR {
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tag "$meta.run"
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label 'process_medium'
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5-
conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
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conda "bioconda::bioconductor-dada2=1.28.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
7-
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.28.0--r43hf17093f_0' :
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'biocontainers/bioconductor-dada2:1.28.0--r43hf17093f_0' }"
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input:
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tuple val(meta), path(errormodel)

‎modules/local/picrust.nf

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Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@ process PICRUST {
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tag "${seq},${abund}"
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label 'process_medium'
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5-
conda "bioconda::picrust2=2.5.0"
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conda "bioconda::picrust2=2.5.2"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/picrust2:2.5.0--pyhdfd78af_0' :
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'biocontainers/picrust2:2.5.0--pyhdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/picrust2:2.5.2--pyhdfd78af_0' :
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'biocontainers/picrust2:2.5.2--pyhdfd78af_0' }"
99

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input:
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path(seq)

‎modules/local/qiime2_alphararefaction.nf

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process QIIME2_ALPHARAREFACTION {
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label 'process_low'
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4-
container "qiime2/core:2022.11"
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container "qiime2/core:2023.7"
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_ancom_asv.nf

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@@ -5,7 +5,7 @@ process QIIME2_ANCOM_ASV {
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label 'process_long'
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label 'error_ignore'
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8-
container "qiime2/core:2022.11"
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container "qiime2/core:2023.7"
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_ancom_tax.nf

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@@ -3,7 +3,7 @@ process QIIME2_ANCOM_TAX {
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label 'process_medium'
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label 'single_cpu'
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6-
container "qiime2/core:2022.11"
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container "qiime2/core:2023.7"
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// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_barplot.nf

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process QIIME2_BARPLOT {
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label 'process_low'
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4-
container "qiime2/core:2022.11"
4+
container "qiime2/core:2023.7"
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66
// Exit if running this module with -profile conda / -profile mamba
77
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_classify.nf

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@@ -2,7 +2,7 @@ process QIIME2_CLASSIFY {
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tag "${repseq},${trained_classifier}"
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label 'process_high'
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5-
container "qiime2/core:2022.11"
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container "qiime2/core:2023.7"
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77
// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_diversity_adonis.nf

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@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ADONIS {
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tag "${core.baseName} - ${formula}"
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label 'process_low'
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5-
container "qiime2/core:2022.11"
5+
container "qiime2/core:2023.7"
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77
// Exit if running this module with -profile conda / -profile mamba
88
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_diversity_alpha.nf

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@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_ALPHA {
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tag "${core.baseName}"
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label 'process_low'
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5-
container "qiime2/core:2022.11"
5+
container "qiime2/core:2023.7"
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77
// Exit if running this module with -profile conda / -profile mamba
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if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_diversity_beta.nf

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Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETA {
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tag "${core.baseName} - ${category}"
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label 'process_low'
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5-
container "qiime2/core:2022.11"
5+
container "qiime2/core:2023.7"
66

77
// Exit if running this module with -profile conda / -profile mamba
88
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_diversity_betaord.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ process QIIME2_DIVERSITY_BETAORD {
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tag "${core.baseName}"
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label 'process_low'
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5-
container "qiime2/core:2022.11"
5+
container "qiime2/core:2023.7"
66

77
// Exit if running this module with -profile conda / -profile mamba
88
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

‎modules/local/qiime2_diversity_core.nf

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process QIIME2_DIVERSITY_CORE {
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label 'process_low'
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4-
container "qiime2/core:2022.11"
4+
container "qiime2/core:2023.7"
55

66
// Exit if running this module with -profile conda / -profile mamba
77
if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

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