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Merge pull request #604 from nf-core/dev
Release 2.6.1
2 parents 9ac22ba + cf80e34 commit 3b252d2

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‎.github/workflows/ci.yml

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@@ -32,7 +32,7 @@ jobs:
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if [[ "${{ github.event_name }}" == "pull_request" && "${{ github.base_ref }}" == "dev" && "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
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echo matrix='["latest-everything"]' | tee -a $GITHUB_OUTPUT
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else
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echo matrix='["latest-everything", "22.10.1"]' | tee -a $GITHUB_OUTPUT
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echo matrix='["latest-everything", "23.04.0"]' | tee -a $GITHUB_OUTPUT
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fi
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test:

‎CHANGELOG.md

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## nf-core/ampliseq version 2.6.1 - 2023-06-27
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### `Fixed`
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- [#603](https://github.com/nf-core/ampliseq/pull/603) - Fix all containers registry
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## nf-core/ampliseq version 2.6.0 - 2023-06-27
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### `Added`

‎README.md

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[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841)
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[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420)
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
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[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
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[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)

‎conf/test_full.config

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----------------------------------------------------------------------------------------
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*/
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cleanup = true
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params {
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config_profile_name = 'Full test profile'
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config_profile_description = 'Full test dataset to check pipeline function'

‎modules.json

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"nf-core": {
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["modules"]
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},
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"cutadapt": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "0efbaeb95c58da5a1096c99b5e919bc0c99cc952",
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"installed_by": ["modules"]
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},
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"epang/place": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"epang/split": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["modules"]
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},
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"gappa/examineassign": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"gappa/examinegraft": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"gappa/examineheattree": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"hmmer/eslalimask": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"hmmer/eslreformat": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"hmmer/hmmalign": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"hmmer/hmmbuild": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["fasta_newick_epang_gappa"]
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},
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"mafft": {
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"branch": "master",
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"git_sha": "b265b4ff6a35b133b963b4eaddfca0ffb3395236",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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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": "f2d63bd5b68925f98f572eed70993d205cc694b7",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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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": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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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": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"installed_by": ["modules"]
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}
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}
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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": "6ad90f5583fb375c60a913a24ed1c79339efc019",
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"git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
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"installed_by": ["subworkflows"]
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}
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}

‎modules/local/assignsh.nf

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conda "conda-forge::pandas=1.1.5"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
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'quay.io/biocontainers/pandas:1.1.5' }"
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'biocontainers/pandas:1.1.5' }"
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input:
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path asvtable

‎modules/local/barrnap.nf

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conda "bioconda::barrnap=0.9"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/barrnap:0.9--hdfd78af_4' :
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'quay.io/biocontainers/barrnap:0.9--hdfd78af_4' }"
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'biocontainers/barrnap:0.9--hdfd78af_4' }"
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path(fasta)

‎modules/local/barrnapsummary.nf

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conda "conda-forge::python=3.9"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/python:3.9' :
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'quay.io/biocontainers/python:3.9' }"
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'biocontainers/python:3.9' }"
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path predictions

‎modules/local/combine_table.nf

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@@ -4,7 +4,7 @@ process COMBINE_TABLE {
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conda "bioconda::bioconductor-biostrings=2.58.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
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'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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path(table)

‎modules/local/cutadapt_summary_merge.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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val(action)

‎modules/local/dada2_addspecies.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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path(taxtable)

‎modules/local/dada2_denoising.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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tuple val(meta), path("filtered/*"), path(errormodel)

‎modules/local/dada2_err.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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tuple val(meta), path(reads)

‎modules/local/dada2_filtntrim.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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tuple val(meta), path(reads), val(trunclenf), val(trunclenr)

‎modules/local/dada2_merge.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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path(files)

‎modules/local/dada2_quality.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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‎modules/local/dada2_rmchimera.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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‎modules/local/dada2_stats.nf

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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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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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@@ -5,7 +5,7 @@ process DADA2_TAXONOMY {
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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' :
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'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
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‎modules/local/filter_codons.nf

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@@ -5,7 +5,7 @@ process FILTER_CODONS {
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conda "conda-forge::pandas=1.1.5"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pandas:1.1.5':
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'quay.io/biocontainers/pandas:1.1.5' }"
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'biocontainers/pandas:1.1.5' }"
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path(fasta)

‎modules/local/filter_len_asv.nf

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@@ -5,7 +5,7 @@ process FILTER_LEN_ASV {
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conda "bioconda::bioconductor-biostrings=2.58.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
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'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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‎modules/local/filter_ssu.nf

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@@ -5,7 +5,7 @@ process FILTER_SSU {
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conda "bioconductor::biostrings=2.58.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bioconductor-biostrings:2.58.0--r40h037d062_0' :
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'quay.io/biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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'biocontainers/bioconductor-biostrings:2.58.0--r40h037d062_0' }"
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‎modules/local/filter_stats.nf

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@@ -4,7 +4,7 @@ process FILTER_STATS {
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conda "conda-forge::pandas=1.1.5"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
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'quay.io/biocontainers/pandas:1.1.5' }"
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'biocontainers/pandas:1.1.5' }"
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‎modules/local/format_fastainput.nf

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@@ -4,7 +4,7 @@ process FORMAT_FASTAINPUT {
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conda "conda-forge::sed=4.7"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
7-
'docker.io/ubuntu:20.04' }"
7+
'nf-core/ubuntu:20.04' }"
88

99
input:
1010
path(fastain)

‎modules/local/format_pplacetax.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ process FORMAT_PPLACETAX {
55
conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
77
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
8-
'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
8+
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
99

1010
input:
1111
tuple val(meta), path(tax)

‎modules/local/format_taxresults.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ process FORMAT_TAXRESULTS {
44
conda "conda-forge::pandas=1.1.5"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/pandas:1.1.5' :
7-
'quay.io/biocontainers/pandas:1.1.5' }"
7+
'biocontainers/pandas:1.1.5' }"
88

99
input:
1010
path(taxtable)

‎modules/local/format_taxresults_sintax.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ process FORMAT_TAXRESULTS_SINTAX {
44
conda "conda-forge::python=3.9"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/python:3.9' :
7-
'quay.io/biocontainers/python:3.9' }"
7+
'biocontainers/python:3.9' }"
88

99
input:
1010
tuple val(meta), path(taxtable)

‎modules/local/itsx_cutasv.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ process ITSX_CUTASV {
44
conda "bioconda::itsx=1.1.3"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/itsx:1.1.3--hdfd78af_1' :
7-
'quay.io/biocontainers/itsx:1.1.3--hdfd78af_1' }"
7+
'biocontainers/itsx:1.1.3--hdfd78af_1' }"
88

99
input:
1010
path fasta

‎modules/local/merge_stats.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ process MERGE_STATS {
44
conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
55
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
66
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
7-
'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
7+
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
88

99
input:
1010
path('file1.tsv')

‎modules/local/metadata_all.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ process METADATA_ALL {
55
conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
77
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
8-
'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
8+
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
99

1010
input:
1111
path(metadata)

‎modules/local/metadata_pairwise.nf

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ process METADATA_PAIRWISE {
55
conda "bioconda::bioconductor-dada2=1.22.0 conda-forge::r-digest=0.6.30"
66
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
77
'https://depot.galaxyproject.org/singularity/bioconductor-dada2:1.22.0--r41h399db7b_0' :
8-
'quay.io/biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
8+
'biocontainers/bioconductor-dada2:1.22.0--r41h399db7b_0' }"
99

1010
input:
1111
path(metadata)

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