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Merge branch 'oncocnv-#7657' of github.com:nf-core/modules into oncocnv-#7657 
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‎modules/nf-core/antismash/Dockerfile

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FROM quay.io/biocontainers/antismash:8.0.0--pyhdfd78af_0
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## Speeds up slightly builds: https://github.com/antismash/antismash/issues/837#issuecomment-2893858536
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## From: https://github.com/antismash/containers/blob/main/standalone-lite/Dockerfile#L25
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RUN mkdir /matplotlib && MPLCONFIGDIR=/matplotlib python3 -c "import matplotlib.pyplot as plt" && chmod -R a+rw /matplotlib
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# Download the antiSMASH database, needed for the prepare-data process
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# Prepare the antiSMASH cache and other bits it needs to run properly
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# Remove the databases to reduce the container size
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RUN download-antismash-databases && antismash --prepare-data && antismash --check-prereqs && rm -rf /usr/local/lib/python3.11/site-packages/antismash/databases
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RUN python -c "from antismash.modules.nrps_pks import prepare_data; prepare_data()" && \
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cp /usr/local/lib/python3.11/site-packages/antismash/modules/nrps_pks/data/terminals/*.brawn_cache /usr/local/lib/python3.11/site-packages/antismash/modules/nrps_pks/data/
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‎modules/nf-core/antismash/README.md

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# Updating the docker container and making a new module release
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antiSMASH is an open source tool.
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The developers do provide two premade docker containers, one that contains a very large database and one that does not.
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The database containing version takes an extremely long time to pull as it's multiple gigabytes in size.
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While theoretically we could use the one without the database, and we would prefer to use a container that is sync with the conda recipe.
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Unfortunately, the default biocontainer recipe does not work out of the box, as the tool requires caching information to be stored inside the installation directories of the tool.
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This caching procedure happens after database downloading, however the database does not fit on the bioconda/biocontainer CI nodes, thus the caching step cannot be executed.
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Therefore, when supplying an externally downloaded database to the container, the tool tries to update the cache locations inside the installation directories which thus fails as containers are read only.
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Therefore, for docker and singularity containers, we need to create a new container based on the biocontainers container, however we locally download the database, generate the cache within the container, _but_ then remove the database before finishing the build.
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_Thanks to @mberacochea for finding the solution and providing the Dockerfile below!_
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Updating the antiSMASH version in the container and pushing the update to Dockerhub needs to be done manually.
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1. Ensure the user that will push the container has access to the nf-core organization on Dockerhub.
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2. Change into the `modules/nf-core/antismash` directory:
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```bash
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cd modules/nf-core/antismash
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```
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3. Create and test the container:
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```bash
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docker build . -t quay.io/nf-core/antismash:<version>
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```
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4. Push the container to Quay:
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```bash
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docker push quay.io/nf-core/antismash:8.0.0
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```
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5. On [https://quay.io/organization/nf-core](https://quay.io/organization/nf-core), select the new repository, press actions and make public.

‎modules/nf-core/antismash/antismash/environment.yml

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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- "bioconda::antismash=8.0.0"

‎modules/nf-core/antismash/antismash/main.nf

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process ANTISMASH_ANTISMASH {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "nf-core/antismash:8.0.0"
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input:
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tuple val(meta), path(sequence_input)
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path databases
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path gff
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output:
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tuple val(meta), path("${prefix}/clusterblast/*_c*.txt"), optional: true, emit: clusterblast_file
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tuple val(meta), path("${prefix}/{css,images,js}"), emit: html_accessory_files
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tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html"), optional: true, emit: knownclusterblast_html
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tuple val(meta), path("${prefix}/knownclusterblast/"), optional: true, emit: knownclusterblast_dir
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tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt"), optional: true, emit: knownclusterblast_txt
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tuple val(meta), path("${prefix}/svg/clusterblast*.svg"), optional: true, emit: svg_files_clusterblast
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tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg"), optional: true, emit: svg_files_knownclusterblast
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tuple val(meta), path("${prefix}/*.gbk"), emit: gbk_input
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tuple val(meta), path("${prefix}/*.json"), emit: json_results
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tuple val(meta), path("${prefix}/*.log"), emit: log
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tuple val(meta), path("${prefix}/*.zip"), emit: zip
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tuple val(meta), path("${prefix}/*region*.gbk"), optional: true, emit: gbk_results
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tuple val(meta), path("${prefix}/clusterblastoutput.txt"), optional: true, emit: clusterblastoutput
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tuple val(meta), path("${prefix}/index.html"), emit: html
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tuple val(meta), path("${prefix}/knownclusterblastoutput.txt"), optional: true, emit: knownclusterblastoutput
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tuple val(meta), path("${prefix}/regions.js"), emit: json_sideloading
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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gff_flag = gff ? "--genefinding-gff3 ${gff}" : ""
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"""
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## We specifically do not include on-the-fly annotations (--genefinding-tool none) as
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## this should be run as a separate module for versioning purposes
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antismash \\
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${args} \\
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${gff_flag} \\
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-c ${task.cpus} \\
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--output-dir ${prefix} \\
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--output-basename ${prefix} \\
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--genefinding-tool none \\
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--logfile ${prefix}/${prefix}.log \\
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--databases ${databases} \\
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${sequence_input}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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antismash: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g')
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END_VERSIONS
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"""
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stub:
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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"""
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mkdir -p ${prefix}/css
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mkdir ${prefix}/images
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mkdir ${prefix}/js
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touch ${prefix}/NZ_CP069563.1.region001.gbk
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touch ${prefix}/NZ_CP069563.1.region002.gbk
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touch ${prefix}/css/bacteria.css
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touch ${prefix}/genome.gbk
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touch ${prefix}/genome.json
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touch ${prefix}/genome.zip
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touch ${prefix}/images/about.svg
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touch ${prefix}/index.html
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touch ${prefix}/js/antismash.js
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touch ${prefix}/js/jquery.js
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touch ${prefix}/regions.js
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touch ${prefix}/test.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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antismash: \$(echo \$(antismash --version) | sed 's/antiSMASH //;s/-.*//g')
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END_VERSIONS
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"""
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}

‎modules/nf-core/antismash/antismash/meta.yml

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name: antismash_antismash
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description: |
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antiSMASH allows the rapid genome-wide identification, annotation
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and analysis of secondary metabolite biosynthesis gene clusters.
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keywords:
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- secondary metabolites
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- BGC
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- biosynthetic gene cluster
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- genome mining
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- NRPS
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- RiPP
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- antibiotics
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- prokaryotes
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- bacteria
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- eukaryotes
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- fungi
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- antismash
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tools:
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- antismash:
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description: "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell"
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homepage: "https://docs.antismash.secondarymetabolites.org"
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documentation: "https://docs.antismash.secondarymetabolites.org"
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tool_dev_url: "https://github.com/antismash/antismash"
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doi: "10.1093/nar/gkab335"
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licence: ["AGPL v3"]
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identifier: biotools:antismash
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- sequence_input:
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type: file
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description: Nucleotide sequence file (annotated)
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pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
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- - databases:
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type: directory
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description: |
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Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
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"data/databases")
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pattern: "*/"
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- - gff:
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type: file
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description: Optional GFF3 file containing premade annotations of the input sequence
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pattern: "*.gff"
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output:
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- clusterblast_file:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/clusterblast/*_c*.txt:
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type: file
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description: Output of ClusterBlast algorithm
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pattern: "clusterblast/*_c*.txt"
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- html_accessory_files:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/{css,images,js}:
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type: directory
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description: Accessory files for the HTML output
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pattern: "{css/,images/,js/}"
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- knownclusterblast_html:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/knownclusterblast/region*/ctg*.html:
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type: file
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description: Tables with MIBiG hits in HTML format
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pattern: "knownclusterblast/region*/ctg*.html"
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- knownclusterblast_dir:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/knownclusterblast/:
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type: directory
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description: Directory with MIBiG hits
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pattern: "knownclusterblast/"
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- knownclusterblast_txt:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/knownclusterblast/*_c*.txt:
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type: file
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description: Tables with MIBiG hits
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pattern: "knownclusterblast/*_c*.txt"
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- svg_files_clusterblast:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/svg/clusterblast*.svg:
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type: file
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description: SVG images showing the % identity of the aligned hits against their
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queries
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pattern: "svg/clusterblast*.svg"
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- svg_files_knownclusterblast:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/svg/knownclusterblast*.svg:
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type: file
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description: SVG images showing the % identity of the aligned hits against their
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queries
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pattern: "svg/knownclusterblast*.svg"
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- gbk_input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*.gbk:
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type: file
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description: Nucleotide sequence and annotations in GenBank format; converted
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from input file
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pattern: "*.gbk"
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- json_results:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*.json:
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type: file
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description: Nucleotide sequence and annotations in JSON format; converted from
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GenBank file (gbk_input)
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pattern: "*.json"
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- log:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*.log:
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type: file
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description: Contains all the logging output that antiSMASH produced during
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its run
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pattern: "*.log"
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- zip:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*.zip:
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type: file
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description: Contains a compressed version of the output folder in zip format
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pattern: "*.zip"
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- gbk_results:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/*region*.gbk:
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type: file
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description: Nucleotide sequence and annotations in GenBank format; one file
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per antiSMASH hit
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pattern: "*region*.gbk"
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- clusterblastoutput:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/clusterblastoutput.txt:
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type: file
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description: Raw BLAST output of known clusters previously predicted by antiSMASH
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using the built-in ClusterBlast algorithm
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pattern: "clusterblastoutput.txt"
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- html:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/index.html:
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type: file
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description: Graphical web view of results in HTML format
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patterN: "index.html"
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- knownclusterblastoutput:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/knownclusterblastoutput.txt:
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type: file
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description: Raw BLAST output of known clusters of the MIBiG database
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pattern: "knownclusterblastoutput.txt"
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- json_sideloading:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ${prefix}/regions.js:
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type: file
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description: Sideloaded annotations of protoclusters and/or subregions (see
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antiSMASH documentation "Annotation sideloading")
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pattern: "regions.js"
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- versions:
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- versions.yml:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@jasmezz"
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maintainers:
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- "@jasmezz"
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- "@jfy133"

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