Initial module creation

modules/antismash/antismashlite/main.nf

@@ -0,0 +1,58 @@
+process ANTISMASH_ANTISMASHLITE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
+        'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(sequence_input)
+    path(databases)
+
+    output:
+    tuple val(meta), path("${prefix}/clusterblast/*_c*.txt")                 , optional: true, emit: clusterblast_file
+    tuple val(meta), path("$prefix/css/*.css")                               , emit: css_file
+    tuple val(meta), path("$prefix/images")                                  , emit: image_directory
+    tuple val(meta), path("$prefix/js/*.js")                                 , emit: javascript
+    tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html")   , optional: true, emit: knownclusterblast_html
+    tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt")            , optional: true, emit: knownclusterblast_txt
+    tuple val(meta), path("${prefix}/svg/clusterblast*.svg")                 , optional: true, emit: svg_files_clusterblast
+    tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg")            , optional: true, emit: svg_files_knownclusterblast
+    tuple val(meta), path("$prefix/*.gbk")                                   , emit: gbk_input
+    tuple val(meta), path("$prefix/*.json")                                  , emit: json_results
+    tuple val(meta), path("$prefix/*.log")                                   , emit: log
+    tuple val(meta), path("$prefix/*.zip")                                   , emit: zip
+    tuple val(meta), path("$prefix/*region*.gbk")                            , emit: gbk_results
+    tuple val(meta), path("${prefix}/clusterblastoutput.txt")                , optional: true, emit: clusterblastoutput
+    tuple val(meta), path("$prefix/index.html")                              , emit: html
+    tuple val(meta), path("${prefix}/knownclusterblastoutput.txt")           , optional: true, emit: knownclusterblastoutput
+    tuple val(meta), path("$prefix/regions.js")                              , emit: json_sideloading
+    path "versions.yml"                                                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
+
+    """
+    ## We specifically do not include annotations (--genefinding-tool none) as
+    ## this should be run as a separate module for versioning purposes
+    antismash \\
+        $sequence_input \\
+        $args \\
+        -c $task.cpus \\
+        --output-dir $prefix \\
+        --genefinding-tool none \\
+        --logfile $prefix/${prefix}.log \\
+        --databases $databases
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        antismash: \$(antismash --version | sed 's/antiSMASH //')
+    END_VERSIONS
+    """
+}

modules/antismash/antismashlite/meta.yml

@@ -0,0 +1,121 @@
+name: antismash_antismashlite
+description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters.
+keywords:
+  - secondary metabolites
+  - BGC
+  - biosynthetic gene cluster
+  - genome mining
+  - NRPS
+  - RiPP
+  - antibiotics
+  - prokaryotes
+  - bacteria
+  - eukaryotes
+  - fungi
+  - antismash
+
+tools:
+  - antismashlite:
+      description: "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell"
+      homepage: "https://docs.antismash.secondarymetabolites.org"
+      documentation: "https://docs.antismash.secondarymetabolites.org"
+      tool_dev_url: "https://github.com/antismash/antismash"
+      doi: "10.1093/nar/gkab335"
+      licence: "['AGPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sequence_input:
+      type: file
+      description: nucleotide sequence file (annotated)
+      pattern: "*.{gbk, gb, gbff, genbank, embl}"
+  - databases:
+      type: directory
+      description: downloaded antismash databases e.g. data/databases
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - clusterblast_file:
+      type: file
+      description: Output of ClusterBlast algorithm
+      pattern: "clusterblast/*_c*.txt"
+  - css_file:
+      type: file
+      description: Style sheet containing the formatting of HTML output
+      pattern: "css/*.css"
+  - image_directory:
+      type: directory
+      description: image files for web view of antiSMASH results
+      pattern: "images"
+  - javascript:
+      type: file
+      description: JavaScript files
+      pattern: "js/*.js"
+  - knownclusterblast_html:
+      type: file
+      description: Tables with MIBiG hits in HTML format
+      pattern: "knownclusterblast/region*/ctg*.html"
+  - knownclusterblast_txt:
+      type: file
+      description: Tables with MIBiG hits
+      pattern: "knownclusterblast/*_c*.txt"
+  - svg_files_clusterblast:
+      type: file
+      description: SVG image showing the % identity of the aligned hits against their queries
+      pattern: "svg/clusterblast*.svg"
+  - svg_files_knownclusterblast:
+      type: file
+      description: SVG image showing the % identity of the aligned hits against their queries
+      pattern: "svg/knownclusterblast*.svg"
+  - gbk_input:
+      type: file
+      description: Nucleotide sequence + annotations in GenBank file format; converted from input file
+      pattern: "*.gbk"
+  - json_results:
+      type: file
+      description: Simple representation of all detected areas during the antiSMASH run in JSON format
+      pattern: "*.json"
+  - log:
+      type: file
+      description: Contains all the logging output that antiSMASH produced during its run
+      pattern: "*.log"
+  - zip:
+      type: file
+      description: Contains a compressed version of the folder in zip format
+      pattern: "*.zip"
+  - gbk_results:
+      type: file
+      description: Nucleotide sequence + annotations in GenBank file format; one file per antiSMASH hit
+      pattern: "*region*.gbk"
+  - clusterblastoutput:
+      type: file
+      description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
+      pattern: "clusterblastoutput.txt"
+  - html:
+      type: file
+      description: Graphical web view of results in HTML format
+      patterN: "index.html"
+  - knownclusterblastoutput:
+      type: file
+      description: Raw BLAST output of known clusters of the MIBiG database
+      pattern: "knownclusterblastoutput.txt"
+  - json_sideloading:
+      type: file
+      description: Sideloaded annotations of protoclusters and/or subregions (see documentation "Annotation sideloading")
+      pattern: "regions.js"
+
+authors:
+  - "@jasmezz"

tests/config/pytest_modules.yml

@@ -42,6 +42,10 @@ amrfinderplus/update:
   - modules/amrfinderplus/update/**
   - tests/modules/amrfinderplus/update/**
 
+antismash/antismashlite:
+  - modules/antismash/antismashlite/**
+  - tests/modules/antismash/antismashlite/**
+
 antismash/antismashlitedownloaddatabases:
   - modules/antismash/antismashlitedownloaddatabases/**
   - tests/modules/antismash/antismashlitedownloaddatabases/**

tests/modules/antismash/antismashlite/main.nf

@@ -0,0 +1,49 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+//include { GUNZIP } from '../../../modules/gunzip/main.nf'
+include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
+include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
+include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
+include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
+include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
+include { PROKKA } from '../../../modules/prokka/main.nf'
+
+workflow test_antismashlite {
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_gbff_gz'], checkIfExists: true) ]
+
+    input_antismash_db1 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
+    ]
+
+        input_antismash_db2 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
+    ]
+
+        input_antismash_db3 = [
+        [],
+        file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
+    ]
+
+    UNTAR1 ( input_antismash_db1 )
+    UNTAR2 ( input_antismash_db2 )
+    UNTAR3 ( input_antismash_db3 )
+    ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] },  UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
+    ANTISMASH_ANTISMASHLITE ( input, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database )
+}
+
+//workflow test_prokka_antismashlite {
+//     input_gunzip = [ [ id:'test' ], // meta map
+//             file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true) ]
+
+//     GUNZIP ( input_gunzip )
+//     PROKKA ( GUNZIP.out.gunzip, [], [] )
+//     ANTISMASHLITEDOWNLOADDATABASES ()
+//     ANTISMASH ( PROKKA.out.gbk )
+// }
+

tests/modules/antismash/antismashlite/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/antismash/antismashlite/test.yml

@@ -0,0 +1,37 @@
+- name: antismash antismashlite test_antismashlite
+  command: nextflow run ./tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config
+  tags:
+    - antismash/antismashlite
+    - antismash
+  files:
+    - path: output/antismash/test/NZ_CP069563.1.region001.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/NZ_CP069563.1.region002.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/css/bacteria.css
+      md5sum: 8b3c2f8b143d5245a5f42f55803c532c
+    - path: output/antismash/test/genome.gbk
+      contains: ['/tool="antismash"']
+    - path: output/antismash/test/genome.json
+      contains: ['{"version": "6.0.1", "input_file": "genome.gbff.gz", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
+    - path: output/antismash/test/genome.zip
+    - path: output/antismash/test/index.html
+      md5sum: 4792f0f4faf318035fbec5b4bf0ff76e
+    - path: output/antismash/test/js/antismash.js
+      md5sum: 58e90c3d783ae014cc3d51849bcb50a2
+    - path: output/antismash/test/js/jquery.js
+      md5sum: 397754ba49e9e0cf4e7c190da78dda05
+    - path: output/antismash/test/js/jquery.tablesorter.min.js
+      md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
+    - path: output/antismash/test/regions.js
+      md5sum: dfc82025379d87df63fbfce734e67725
+    - path: output/antismash/test/test.log
+      contains: ['antiSMASH version: 6.0.1']
+    - path: output/antismash/versions.yml
+      md5sum: 7151dfd4d39173338397b2dab50acf8e
+    - path: output/untar1/versions.yml
+      md5sum: 42c2c02eb6b5bc47b151bdd2c49bbb2d
+    - path: output/untar2/versions.yml
+      md5sum: 5a608b991b7d3e55cc43206939991a2d
+    - path: output/untar3/versions.yml
+      md5sum: ec74401950e3820b7575840571a6f00c