Merge branch 'nf-core:master' into master

modules/abricate/run/main.nf

@@ -0,0 +1,34 @@
+process ABRICATE_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
+        'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
+
+    input:
+    tuple val(meta), path(assembly)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: report
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    abricate \\
+        $assembly \\
+        $args \\
+        --threads $task.cpus > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
+    END_VERSIONS
+    """
+}

modules/abricate/run/meta.yml

@@ -0,0 +1,43 @@
+name: abricate_run
+description: Screen assemblies for antimicrobial resistance against multiple databases
+keywords:
+  - bacteria
+  - assembly
+  - antimicrobial reistance
+tools:
+  - abricate:
+      description: Mass screening of contigs for antibiotic resistance genes
+      homepage: https://github.com/tseemann/abricate
+      documentation: https://github.com/tseemann/abricate
+      tool_dev_url: https://github.com/tseemann/abricate
+      doi: ""
+      licence: ['GPL v2', 'GPL v2']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - assembly:
+      type: file
+      description: FASTA, GenBank or EMBL formatted file
+      pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+
+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"
+  - report:
+      type: file
+      description: Tab-delimited report of results
+      pattern: "*.{txt}"
+
+authors:
+  - "@rpetit3"

modules/abricate/summary/main.nf

@@ -0,0 +1,33 @@
+process ABRICATE_SUMMARY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/abricate%3A1.0.1--ha8f3691_1':
+        'quay.io/biocontainers/abricate:1.0.1--ha8f3691_1' }"
+
+    input:
+    tuple val(meta), path(reports)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: report
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    abricate \\
+        --summary \\
+        $reports > ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
+    END_VERSIONS
+    """
+}

modules/abricate/summary/meta.yml

@@ -0,0 +1,43 @@
+name: abricate_summary
+description: Screen assemblies for antimicrobial resistance against multiple databases
+keywords:
+  - bacteria
+  - assembly
+  - antimicrobial reistance
+tools:
+  - abricate:
+      description: Mass screening of contigs for antibiotic resistance genes
+      homepage: https://github.com/tseemann/abricate
+      documentation: https://github.com/tseemann/abricate
+      tool_dev_url: https://github.com/tseemann/abricate
+      doi: ""
+      licence: ['GPL v2', 'GPL v2']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - assembly:
+      type: file
+      description: FASTA, GenBank or EMBL formatted file
+      pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+
+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"
+  - summary:
+      type: file
+      description: Tab-delimited report of aggregated results
+      pattern: "*.{txt}"
+
+authors:
+  - "@rpetit3"

modules/amrfinderplus/run/main.nf

@@ -0,0 +1,55 @@
+process AMRFINDERPLUS_RUN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path db
+
+    output:
+    tuple val(meta), path("${prefix}.tsv")          , emit: report
+    tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    prefix = task.ext.prefix ?: "${meta.id}"
+    organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
+    fasta_name = fasta.getName().replace(".gz", "")
+    fasta_param = "-n"
+    if (meta.containsKey("is_proteins")) {
+        if (meta.is_proteins) {
+            fasta_param = "-p"
+        }
+    }
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    mkdir amrfinderdb
+    tar xzvf $db -C amrfinderdb
+
+    amrfinder \\
+        $fasta_param $fasta_name \\
+        $organism_param \\
+        $args \\
+        --database amrfinderdb \\
+        --threads $task.cpus > ${prefix}.tsv
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        amrfinderplus: \$(amrfinder --version)
+    END_VERSIONS
+    """
+}

modules/amrfinderplus/run/meta.yml

@@ -0,0 +1,51 @@
+name: amrfinderplus_run
+description: Identify antimicrobial resistance in gene or protein sequences
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - amrfinderplus:
+      description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
+      homepage: https://github.com/ncbi/amr/wiki
+      documentation: https://github.com/ncbi/amr/wiki
+      tool_dev_url: https://github.com/ncbi/amr
+      doi: "10.1038/s41598-021-91456-0"
+      licence: ['Public Domain']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleotide or protein sequences in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+  - db:
+      type: file
+      description: A compressed tarball of the AMRFinderPlus database to query
+      pattern: "*.tar.gz"
+
+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"
+  - report:
+      type: file
+      description: AMRFinder+ final report
+      pattern: "*.tsv"
+  - mutation_report:
+      type: file
+      description: Report of organism-specific point-mutations
+      pattern: "*-mutations.tsv"
+
+authors:
+  - "@rpetit3"

modules/amrfinderplus/update/main.nf

@@ -0,0 +1,29 @@
+process AMRFINDERPLUS_UPDATE {
+    tag "update"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
+
+    output:
+    path "amrfinderdb.tar.gz", emit: db
+    path "versions.yml"      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    mkdir amrfinderdb
+    amrfinder_update -d amrfinderdb
+    tar czvf amrfinderdb.tar.gz -C \$(readlink amrfinderdb/latest) ./
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        amrfinderplus: \$(amrfinder --version)
+    END_VERSIONS
+    """
+}

modules/amrfinderplus/update/meta.yml

@@ -0,0 +1,37 @@
+name: amrfinderplus_update
+description: Identify antimicrobial resistance in gene or protein sequences
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - amrfinderplus:
+      description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences.
+      homepage: https://github.com/ncbi/amr/wiki
+      documentation: https://github.com/ncbi/amr/wiki
+      tool_dev_url: https://github.com/ncbi/amr
+      doi: "10.1038/s41598-021-91456-0"
+      licence: ['Public Domain']
+
+input:
+  - input_not_required:
+      type: null
+      description: module does not have an input
+
+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"
+  - db:
+      type: file
+      description: The latest AMRFinder+ database in a compressed tarball
+      pattern: "*.tar.gz"
+
+authors:
+  - "@rpetit3"

modules/artic/minion/main.nf

@@ -13,7 +13,8 @@ process ARTIC_MINION {
     path  sequencing_summary
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta")
     path  ("primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed")
-    path  medaka_model
+    path  medaka_model_file
+    val   medaka_model_string
     val   scheme
     val   scheme_version
 
@@ -44,7 +45,7 @@ process ARTIC_MINION {
     if (args.tokenize().contains('--medaka')) {
         fast5   = ""
         summary = ""
-        model = file(medaka_model).exists() ? "--medaka-model ./$medaka_model" : "--medaka-model $medaka_model"
+        model   = medaka_model_file ? "--medaka-model ./$medaka_model_file" : "--medaka-model $medaka_model_string"
     }
     def hd5_plugin_path = task.ext.hd5_plugin_path ? "export HDF5_PLUGIN_PATH=" + task.ext.hd5_plugin_path : "export HDF5_PLUGIN_PATH=/usr/local/lib/python3.6/site-packages/ont_fast5_api/vbz_plugin"
     """

modules/artic/minion/meta.yml

@@ -42,11 +42,16 @@ input:
         bed files containing coordinates of each primer in the scheme,
         relative to the reference genome
       pattern: "*.{scheme.bed}"
-  - medaka_model:
+  - medaka_model_file:
       type: file
       description: |
-        Medaka model to use (if option --medaka is set)
-      pattern: "*.*"
+        Medaka model file to use (if option --medaka is set)
+      pattern: "*.hdf5"
+  - medaka_model_string:
+      type: value
+      description: |
+        Medaka model string to use (if option --medaka is set)
+      pattern: "*"
   - scheme:
       type: value
       description: Name of the primer scheme

modules/fastp/main.nf

@@ -13,7 +13,7 @@ process FASTP {
     val   save_merged
 
     output:
-    tuple val(meta), path('*.trim.fastq.gz')  , emit: reads
+    tuple val(meta), path('*.trim.fastq.gz')  , optional:true, emit: reads
     tuple val(meta), path('*.json')           , emit: json
     tuple val(meta), path('*.html')           , emit: html
     tuple val(meta), path('*.log')            , emit: log

modules/fastp/meta.yml

@@ -22,6 +22,12 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - save_trimmed_fail:
+      type: boolean
+      description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz`
+  - save_merged:
+      type: boolean
+      description: Specify true to save all merged reads to the a file ending in `*.merged.fastq.gz`
 
 output:
   - meta:

modules/gatk4/genotypegvcfs/main.nf

@@ -1,6 +1,6 @@
 process GATK4_GENOTYPEGVCFS {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/ivar/variants/main.nf

@@ -10,6 +10,7 @@ process IVAR_VARIANTS {
     input:
     tuple val(meta), path(bam)
     path  fasta
+    path  fai
     path  gff
     val   save_mpileup
 

modules/ivar/variants/meta.yml

@@ -25,6 +25,10 @@ input:
       type: file
       description: The reference sequence used for mapping and generating the BAM file
       pattern: "*.fa"
+  - fai:
+      type: file
+      description: The index for the reference sequence used for mapping and generating the BAM file
+      pattern: "*.fai"
   - gff:
       type: file
       description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done.

modules/legsta/main.nf

@@ -0,0 +1,33 @@
+process LEGSTA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::legsta=0.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/legsta%3A0.5.1--hdfd78af_2':
+        'quay.io/biocontainers/legsta:0.5.1--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(seqs)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    legsta \\
+        $args \\
+        $seqs > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;')
+    END_VERSIONS
+    """
+}

modules/legsta/meta.yml

@@ -0,0 +1,42 @@
+name: legsta
+description: Typing of clinical and environmental isolates of Legionella pneumophila
+keywords:
+  - bacteria
+  - legionella
+tools:
+  - legsta:
+      description: In silico Legionella pneumophila Sequence Based Typing
+      homepage: https://github.com/tseemann/legsta
+      documentation: https://github.com/tseemann/legsta
+      tool_dev_url: https://github.com/tseemann/legsta
+      doi: ""
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seqs:
+      type: file
+      description: FASTA, GenBank or EMBL formatted files
+      pattern: "*.{fasta,gbk,embl}"
+
+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"
+  - tsv:
+      type: file
+      description: Tab-delimited summary of the results
+      pattern: "*.{tsv}"
+
+authors:
+  - "@rpetit3"

modules/mobsuite/recon/main.nf

@@ -0,0 +1,45 @@
+process MOBSUITE_RECON {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::mob_suite=3.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/mob_suite%3A3.0.3--pyhdfd78af_0':
+        'quay.io/biocontainers/mob_suite:3.0.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("results/chromosome.fasta")    , emit: chromosome
+    tuple val(meta), path("results/contig_report.txt")   , emit: contig_report
+    tuple val(meta), path("results/plasmid_*.fasta")     , emit: plasmids        , optional: true
+    tuple val(meta), path("results/mobtyper_results.txt"), emit: mobtyper_results, optional: true
+    path "versions.yml"                                  , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    mob_recon \\
+        --infile $fasta_name \\
+        $args \\
+        --num_threads $task.cpus \\
+        --outdir results \\
+        --sample_id $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mobsuite: \$(echo \$(mob_recon --version 2>&1) | sed 's/^.*mob_recon //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/mobsuite/recon/meta.yml

@@ -0,0 +1,54 @@
+name: mobsuite_recon
+description: A tool to reconstruct plasmids in bacterial assemblies
+keywords:
+  - bacteria
+  - plasmid
+tools:
+  - mobsuite:
+      description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
+      homepage: https://github.com/phac-nml/mob-suite
+      documentation: https://github.com/phac-nml/mob-suite
+      tool_dev_url: https://github.com/phac-nml/mob-suite
+      doi: "10.1099/mgen.0.000435"
+      licence: ['Apache License, Version 2.0']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: A bacterial genome assembly in FASTA format
+      pattern: "*.{fasta,fa,fna}"
+
+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"
+  - chromosome:
+      type: file
+      description: FASTA file of all contigs found to belong to the chromosome
+      pattern: "chromosome.fasta"
+  - contig_report:
+      type: file
+      description: Assignment of the contig to chromosome or a particular plasmid grouping
+      pattern: "contig_report.txt"
+  - plasmids:
+      type: file
+      description: Each plasmid group is written to an individual FASTA
+      pattern: "plasmid_*.fasta"
+  - mobtyper_results:
+      type: file
+      description: Aggregate MOB-typer report files for all identified plasmid
+      pattern: "mobtyper_results.txt"
+
+authors:
+  - "@rpetit3"

modules/picard/addorreplacereadgroups/main.nf

@@ -0,0 +1,53 @@
+process PICARD_ADDORREPLACEREADGROUPS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args        ?: ''
+    def prefix = task.ext.prefix    ?: "${meta.id}"
+    def ID = task.ext.id            ?: "id"
+    def LIBRARY= task.ext.library   ?: "library"
+    def PLATFORM= task.ext.platform ?: "illumina"
+    def BARCODE= task.ext.barcode   ?: "barcode"
+    def SAMPLE= task.ext.sample     ?: "sample"
+    def INDEX= task.ext.index       ?: "index"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard AddOrReplaceReadGroups] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        AddOrReplaceReadGroups \\
+        -Xmx${avail_mem}g \\
+        --INPUT ${bam} \\
+        --OUTPUT ${prefix}.bam \\
+        -ID ${ID} \\
+        -LB ${LIBRARY} \\
+        -PL ${PLATFORM} \\
+        -PU ${BARCODE} \\
+        -SM ${SAMPLE} \\
+        -CREATE_INDEX true
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard AddOrReplaceReadGroups --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/addorreplacereadgroups/meta.yml

@@ -0,0 +1,46 @@
+name: picard_addorreplacereadgroups
+description: Assigns all the reads in a file to a single new read-group
+keywords:
+  - add
+  - replace
+  - read-group
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Input BAM file
+      pattern: "*.{bam}"
+
+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"
+  - bam:
+      type: file
+      description: Output BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

modules/picard/cleansam/main.nf

@@ -0,0 +1,44 @@
+process PICARD_CLEANSAM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(sam)
+
+    output:
+    tuple val(meta), path("*.sam"), emit: sam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def STRINGENCY = task.ext.stringency ?: "STRICT"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard CleanSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        CleanSam  \\
+        ${args} \\
+        -I ${sam} \\
+        -O ${prefix}.sam \\
+        --VALIDATION_STRINGENCY ${STRINGENCY}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CleanSam --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/cleansam/meta.yml

@@ -0,0 +1,46 @@
+name: picard_cleansam
+description: Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads
+keywords:
+  - clean
+  - sam
+  - bam
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - sam:
+      type: file
+      description: SAM file
+      pattern: "*.{sam}"
+
+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"
+  - sam:
+      type: file
+      description: Cleaned SAM file
+      pattern: "*.{sam}"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

modules/picard/createsequencedictionary/main.nf

@@ -0,0 +1,42 @@
+process PICARD_CREATESEQUENCEDICTIONARY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.dict"), emit: reference_dict
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard CreateSequenceDictionary] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        -Xmx${avail_mem}g \\
+        CreateSequenceDictionary  \\
+        $args \\
+        R=$fasta \\
+        O=${prefix}.dict
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard CreateSequenceDictionary --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/createsequencedictionary/meta.yml

@@ -0,0 +1,45 @@
+name: picard_createsequencedictionary
+description: Creates a sequence dictionary for a reference sequence.
+keywords:
+  - sequence
+  - dictionary
+  - picard
+tools:
+  - picard:
+      description: |
+            Creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+
+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"
+  - dict:
+    type: file
+    description: picard dictionary file
+    pattern: "*.{dict}"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

modules/picard/fixmateinformation/main.nf

@@ -0,0 +1,43 @@
+process PICARD_FIXMATEINFORMATION {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::picard=2.26.9" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/picard:2.26.9--hdfd78af_0' :
+        'quay.io/biocontainers/picard:2.26.9--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def STRINGENCY = task.ext.stringency ?: "STRICT"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Picard FixMateInformation] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    picard \\
+        FixMateInformation \\
+        -Xmx${avail_mem}g \\
+        -I ${bam} \\
+        -O ${prefix}.bam \\
+        --VALIDATION_STRINGENCY ${STRINGENCY}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        picard: \$(picard FixMateInformation --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d:)
+    END_VERSIONS
+    """
+}

modules/picard/fixmateinformation/meta.yml

@@ -0,0 +1,44 @@
+name: picard_fixmateinformation
+description: Verify mate-pair information between mates and fix if needed
+keywords:
+  - mate-pair
+tools:
+  - picard:
+      description: |
+        A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
+        data and formats such as SAM/BAM/CRAM and VCF.
+      homepage: https://broadinstitute.github.io/picard/
+      documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard-
+      tool_dev_url: https://github.com/broadinstitute/picard
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM file
+      pattern: "*.{bam}"
+
+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"
+  - bam:
+      type: file
+      description: mate-pair verified BAM file
+      pattern: "*.{bam}"
+
+authors:
+  - "@sateeshperi"
+  - "@mjcipriano"
+  - "@hseabolt"

modules/rgi/main/main.nf

@@ -0,0 +1,37 @@
+process RGI_MAIN {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::rgi=5.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rgi:5.2.1--pyha8f3691_2':
+        'quay.io/biocontainers/rgi:5.2.1--pyha8f3691_2' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.txt") , emit: tsv
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    rgi \\
+        main \\
+        $args \\
+        --num_threads $task.cpus \\
+        --output_file $prefix \\
+        --input_sequence $fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rgi: \$(rgi main --version)
+    END_VERSIONS
+    """
+}

modules/rgi/main/meta.yml

@@ -0,0 +1,47 @@
+name: rgi_main
+description: Predict antibiotic resistance from protein or nucleotide data
+keywords:
+  - bacteria
+  - fasta
+  - antibiotic resistance
+tools:
+  - rgi:
+      description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website
+      homepage: https://card.mcmaster.ca
+      documentation: https://github.com/arpcard/rgi
+      tool_dev_url: https://github.com/arpcard/rgi
+      doi: "10.1093/nar/gkz935"
+      licence: ['https://card.mcmaster.ca/about']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleotide or protein sequences in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+
+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"
+  - json:
+      type: file
+      description: JSON formatted file with RGI results
+      pattern: "*.{json}"
+  - tsv:
+      type: file
+      description: Tab-delimited file with RGI results
+      pattern: "*.{txt}"
+
+authors:
+  - "@rpetit3"

modules/rseqc/tin/main.nf

@@ -1,6 +1,6 @@
 process RSEQC_TIN {
     tag "$meta.id"
-    label 'process_medium'
+    label 'process_high'
 
     conda (params.enable_conda ? "bioconda::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/sistr/main.nf

@@ -0,0 +1,49 @@
+process SISTR {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::sistr_cmd=1.1.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sistr_cmd:1.1.1--pyh864c0ab_2':
+        'quay.io/biocontainers/sistr_cmd:1.1.1--pyh864c0ab_2' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tab")         , emit: tsv
+    tuple val(meta), path("*-allele.fasta"), emit: allele_fasta
+    tuple val(meta), path("*-allele.json") , emit: allele_json
+    tuple val(meta), path("*-cgmlst.csv")  , emit: cgmlst_csv
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def is_compressed = fasta.getName().endsWith(".gz") ? true : false
+    def fasta_name = fasta.getName().replace(".gz", "")
+    """
+    if [ "$is_compressed" == "true" ]; then
+        gzip -c -d $fasta > $fasta_name
+    fi
+
+    sistr \\
+        --qc \\
+        $args \\
+        --threads $task.cpus \\
+        --alleles-output ${prefix}-allele.json \\
+        --novel-alleles ${prefix}-allele.fasta \\
+        --cgmlst-profiles ${prefix}-cgmlst.csv \\
+        --output-prediction ${prefix} \\
+        --output-format tab \\
+        $fasta_name
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sistr: \$(echo \$(sistr --version 2>&1) | sed 's/^.*sistr_cmd //; s/ .*\$//' )
+    END_VERSIONS
+    """
+}

modules/sistr/meta.yml

@@ -0,0 +1,55 @@
+name: sistr
+description: Serovar prediction of salmonella assemblies
+keywords:
+  - bacteria
+  - fasta
+  - salmonella
+tools:
+  - sistr:
+      description: Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction
+      homepage: https://github.com/phac-nml/sistr_cmd
+      documentation: https://github.com/phac-nml/sistr_cmd
+      tool_dev_url: https://github.com/phac-nml/sistr_cmd
+      doi: "10.1371/journal.pone.0147101"
+      licence: ['Apache-2.0']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleotide or protein sequences in FASTA format
+      pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+
+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"
+  - tsv:
+      type: file
+      description: SISTR serovar prediction
+      pattern: "*.{tsv}"
+  - allele_json:
+      type: file
+      description: Allele sequences and info to JSON
+      pattern: "*.{json}"
+  - allele_fasta:
+      type: file
+      description: FASTA file destination of novel cgMLST alleles
+      pattern: "*.{fasta}"
+  - cgmlst_csv:
+      type: file
+      description: CSV file destination for cgMLST allelic profiles
+      pattern: "*.{csv}"
+
+authors:
+  - "@rpetit3"

modules/vcfanno/main.nf

@@ -9,11 +9,13 @@ process VCFANNO {
 
     input:
     tuple val(meta), path(vcf), path(tbi)
-    path vcfanno_config
+    tuple val(meta), path(vcf_uncompressed)
+    path toml
+    path resource_dir
 
     output:
-    tuple val(meta), path("*.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*_annotated.vcf"), emit: vcf
+    path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,12 +23,15 @@ process VCFANNO {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def input_vcf = vcf_uncompressed ?: vcf
     """
+    ln -sf $resource_dir/* \$(pwd)
+
     vcfanno \\
         -p $task.cpus \\
         $args \\
-        $vcfanno_config \\
-        $vcf \\
+        $toml \\
+        $input_vcf \\
         > ${prefix}_annotated.vcf
 
     cat <<-END_VERSIONS > versions.yml

modules/vcfanno/meta.yml

@@ -5,6 +5,8 @@ keywords:
   - bed
   - annotate
   - variant
+  - lua
+  - toml
 tools:
   - vcfanno:
       description: annotate a VCF with other VCFs/BEDs/tabixed files
@@ -23,19 +25,21 @@ input:
   - vcf:
       type: file
       description: query VCF file
-      pattern: "*.{vcf.gz}"
-  - vcf.tbi:
+      pattern: "*.{vcf, vcf.gz}"
+  - vcf_tabix:
       type: file
-      description: query VCF file index
-      pattern: "*.{vcf.gz.tbi}"
-  - vcfanno_config:
+      description: tabix index of query VCF - only needed if vcf is compressed
+      pattern: "*.vcf.gz.tbi"
+  - toml:
+      type: file
+      description: configuration file
+      pattern: "*.toml"
+  - resource_dir:
       type: file
       description: |
-        A simple configuration file is used to specify both the source files
-        and the set of attributes (in the case of VCF)
-        or columns (in the case of BED or other tab-delimited formats)
-        that should be added to the query file.
-      pattern: "*.{toml}"
+        This directory contains referenced files in the TOML config,
+        and the corresponding indicies e.g. exac.vcf.gz + exac.vcf.gz.tbi,
+        with exception to the lua file.
 
 output:
   - meta:
@@ -50,7 +54,7 @@ output:
   - vcf:
       type: file
       description: Annotated VCF file
-      pattern: "*.{vcf}"
+      pattern: "*.vcf"
 
 authors:
   - "@projectoriented"

tests/config/pytest_modules.yml

@@ -2,6 +2,14 @@ abacas:
   - modules/abacas/**
   - tests/modules/abacas/**
 
+abricate/run:
+  - modules/abricate/run/**
+  - tests/modules/abricate/run/**
+
+abricate/summary:
+  - modules/abricate/summary/**
+  - tests/modules/abricate/summary/**
+
 adapterremoval:
   - modules/adapterremoval/**
   - tests/modules/adapterremoval/**
@@ -18,6 +26,14 @@ amps:
   - modules/amps/**
   - tests/modules/amps/**
 
+amrfinderplus/run:
+  - modules/amrfinderplus/run/**
+  - tests/modules/amrfinderplus/run/**
+
+amrfinderplus/update:
+  - modules/amrfinderplus/update/**
+  - tests/modules/amrfinderplus/update/**
+
 arriba:
   - modules/arriba/**
   - tests/modules/arriba/**
@@ -892,6 +908,10 @@ leehom:
   - modules/leehom/**
   - tests/modules/leehom/**
 
+legsta:
+  - modules/legsta/**
+  - tests/modules/legsta/**
+
 lima:
   - modules/lima/**
   - tests/modules/lima/**
@@ -1020,6 +1040,10 @@ mlst:
   - modules/mlst/**
   - tests/modules/mlst/**
 
+mobsuite/recon:
+  - modules/mobsuite/recon/**
+  - tests/modules/mobsuite/recon/**
+
 mosdepth:
   - modules/mosdepth/**
   - tests/modules/mosdepth/**
@@ -1141,6 +1165,14 @@ phyloflash:
   - modules/phyloflash/**
   - tests/modules/phyloflash/**
 
+picard/addorreplacereadgroups:
+  - modules/picard/addorreplacereadgroups/**
+  - tests/modules/picard/addorreplacereadgroups/**
+
+picard/cleansam:
+  - modules/picard/cleansam/**
+  - tests/modules/picard/cleansam/**
+
 picard/collecthsmetrics:
   - modules/picard/collecthsmetrics/**
   - tests/modules/picard/collecthsmetrics/**
@@ -1153,10 +1185,18 @@ picard/collectwgsmetrics:
   - modules/picard/collectwgsmetrics/**
   - tests/modules/picard/collectwgsmetrics/**
 
+picard/createsequencedictionary:
+  - modules/picard/createsequencedictionary/**
+  - tests/modules/picard/createsequencedictionary/**
+
 picard/filtersamreads:
   - modules/picard/filtersamreads/**
   - tests/modules/picard/filtersamreads/**
 
+picard/fixmateinformation:
+  - modules/picard/fixmateinformation/**
+  - tests/modules/picard/fixmateinformation/**
+
 picard/markduplicates:
   - modules/picard/markduplicates/**
   - tests/modules/picard/markduplicates/**
@@ -1261,6 +1301,10 @@ raxmlng:
   - modules/raxmlng/**
   - tests/modules/raxmlng/**
 
+rgi/main:
+  - modules/rgi/main/**
+  - tests/modules/rgi/main/**
+
 rmarkdownnotebook:
   - modules/rmarkdownnotebook/**
   - tests/modules/rmarkdownnotebook/**
@@ -1425,6 +1469,10 @@ shovill:
   - modules/shovill/**
   - tests/modules/shovill/**
 
+sistr:
+  - modules/sistr/**
+  - tests/modules/sistr/**
+
 snpdists:
   - modules/snpdists/**
   - tests/modules/snpdists/**

tests/config/test_data.config

@@ -154,7 +154,9 @@ params {
                 justhusky_ped                                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky.ped"
                 justhusky_minimal_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz"
                 justhusky_minimal_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/ped/justhusky_minimal.vcf.gz.tbi"
-
+                
+                vcfanno_tar_gz                                 = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno_grch38_module_test.tar.gz"
+                vcfanno_toml                                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
             }
             'pangenome' {
                 pangenome_fa                                  = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"

tests/modules/abricate/run/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf'
+
+workflow test_abricate_run {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    ABRICATE_RUN ( input )
+}

tests/modules/abricate/run/nextflow.config

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

tests/modules/abricate/run/test.yml

@@ -0,0 +1,10 @@
+- name: abricate run
+  command: nextflow run tests/modules/abricate/run -entry test_abricate_run -c tests/config/nextflow.config
+  tags:
+    - abricate
+    - abricate/run
+  files:
+    - path: output/abricate/test.txt
+      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
+    - path: output/abricate/versions.yml
+      md5sum: ae9cafaae96a644bb852e337aa7251f3

tests/modules/abricate/summary/main.nf

@@ -0,0 +1,21 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ABRICATE_RUN } from '../../../../modules/abricate/run/main.nf'
+include { ABRICATE_SUMMARY } from '../../../../modules/abricate/summary/main.nf'
+
+workflow test_abricate_summary {
+
+    inputs = [
+        tuple([ id:'test1', single_end:false ], // meta map
+              file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
+        tuple([ id:'test2', single_end:false ],
+              file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
+    ]
+
+    ABRICATE_RUN ( Channel.fromList(inputs) )
+    ABRICATE_SUMMARY ( 
+        ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
+    )
+}

tests/modules/abricate/summary/nextflow.config

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

tests/modules/abricate/summary/test.yml

@@ -0,0 +1,14 @@
+- name: abricate summary
+  command: nextflow run tests/modules/abricate/summary -entry test_abricate_summary -c tests/config/nextflow.config
+  tags:
+    - abricate
+    - abricate/summary
+  files:
+    - path: output/abricate/test1.txt
+      md5sum: cd07e2953b127aed8d09bf1b2b903a1f
+    - path: output/abricate/test2.txt
+      md5sum: 69af3321b0bc808b7ef85f102395736f
+    - path: output/abricate/test_summary.txt
+      md5sum: a4ec7010e75404ce3a1033f0c4b4a7f9
+    - path: output/abricate/versions.yml
+      md5sum: a18f0471c49e5f25ec0b0c4ad5fab08e

tests/modules/amrfinderplus/run/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf'
+include { AMRFINDERPLUS_RUN } from '../../../../modules/amrfinderplus/run/main.nf'
+
+workflow test_amrfinderplus_run {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    AMRFINDERPLUS_UPDATE ( )
+    AMRFINDERPLUS_RUN ( input, AMRFINDERPLUS_UPDATE.out.db )
+}

tests/modules/amrfinderplus/run/nextflow.config

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

tests/modules/amrfinderplus/run/test.yml

@@ -0,0 +1,11 @@
+- name: amrfinderplus run test_amrfinderplus_run
+  command: nextflow run tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c tests/config/nextflow.config
+  tags:
+    - amrfinderplus/run
+    - amrfinderplus
+  files:
+    - path: output/amrfinderplus/amrfinderdb.tar.gz
+    - path: output/amrfinderplus/test.tsv
+      md5sum: b4d261ace9be7d013c19d1f5c0005bfe
+    - path: output/amrfinderplus/versions.yml
+      md5sum: 642ca04a07d79fe4c4d02348562e3961

tests/modules/amrfinderplus/update/main.nf

@@ -0,0 +1,11 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { AMRFINDERPLUS_UPDATE } from '../../../../modules/amrfinderplus/update/main.nf'
+
+workflow test_amrfinderplus_update {
+
+    AMRFINDERPLUS_UPDATE ( )
+
+}

tests/modules/amrfinderplus/update/nextflow.config

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

tests/modules/amrfinderplus/update/test.yml

@@ -0,0 +1,9 @@
+- name: amrfinderplus update test_amrfinderplus_update
+  command: nextflow run tests/modules/amrfinderplus/update -entry test_amrfinderplus_update -c tests/config/nextflow.config
+  tags:
+    - amrfinderplus
+    - amrfinderplus/update
+  files:
+    - path: output/amrfinderplus/amrfinderdb.tar.gz
+    - path: output/amrfinderplus/versions.yml
+      md5sum: 4db18fa509309db4da0920a7eeaba86c

tests/modules/artic/minion/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { UNTAR } from '../../../../modules/untar/main.nf'
+include { UNTAR        } from '../../../../modules/untar/main.nf'
 include { ARTIC_MINION } from '../../../../modules/artic/minion/main.nf'
 
 workflow test_artic_minion {
@@ -15,9 +15,8 @@ workflow test_artic_minion {
     sequencing_summary = file(params.test_data['sarscov2']['nanopore']['test_sequencing_summary'], checkIfExists: true)
     fasta              = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.reference.fasta', checkIfExists: true)
     bed                = file('https://github.com/artic-network/primer-schemes/raw/master/nCoV-2019/V3/nCoV-2019.primer.bed', checkIfExists: true)
-    dummy_file         = []
 
     fast5_dir = UNTAR ( fast5_tar ).untar
 
-    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, dummy_file, 'nCoV-2019', '3')
+    ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
 }

tests/modules/ivar/variants/main.nf

@@ -11,10 +11,11 @@ workflow test_ivar_variants_no_gff_no_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
     save_mpileup = false
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_no_gff_with_mpileup {
@@ -24,10 +25,11 @@ workflow test_ivar_variants_no_gff_with_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = []
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = []
     save_mpileup = true
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }
 
 workflow test_ivar_variants_with_gff_with_mpileup {
@@ -37,8 +39,9 @@ workflow test_ivar_variants_with_gff_with_mpileup {
         file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
     ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
-    gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    gff   = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     save_mpileup = true
 
-    IVAR_VARIANTS ( input, fasta, gff, save_mpileup )
+    IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup )
 }

tests/modules/legsta/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { LEGSTA } from '../../../modules/legsta/main.nf'
+
+workflow test_legsta {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    LEGSTA ( input )
+}

tests/modules/legsta/nextflow.config

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

tests/modules/legsta/test.yml

@@ -0,0 +1,9 @@
+- name: legsta test_legsta
+  command: nextflow run tests/modules/legsta -entry test_legsta -c tests/config/nextflow.config
+  tags:
+    - legsta
+  files:
+    - path: output/legsta/test.tsv
+      md5sum: c493bdd19335de4828aa8b4e3ce7e1f8
+    - path: output/legsta/versions.yml
+      md5sum: d16c5f6fd68d2bcc2c71954e3342aabe

tests/modules/mobsuite/recon/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOBSUITE_RECON } from '../../../../modules/mobsuite/recon/main.nf'
+
+workflow test_mobsuite_recon {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+
+    MOBSUITE_RECON ( input )
+}

tests/modules/mobsuite/recon/nextflow.config

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

tests/modules/mobsuite/recon/test.yml

@@ -0,0 +1,12 @@
+- name: mobsuite recon test_mobsuite_recon
+  command: nextflow run tests/modules/mobsuite/recon -entry test_mobsuite_recon -c tests/config/nextflow.config
+  tags:
+    - mobsuite/recon
+    - mobsuite
+  files:
+    - path: output/mobsuite/results/chromosome.fasta
+      md5sum: 33b2a0fa321c73c6ba8d8272dd53c6d4
+    - path: output/mobsuite/results/contig_report.txt
+      md5sum: a0ae364a9f2b475f77588d0b3c24b857
+    - path: output/mobsuite/versions.yml
+      md5sum: 7f7a0f8957394b0e526233a0edb8e20a

tests/modules/picard/addorreplacereadgroups/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_ADDORREPLACEREADGROUPS } from '../../../../modules/picard/addorreplacereadgroups/main.nf'
+
+workflow test_picard_addorreplacereadgroups {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_ADDORREPLACEREADGROUPS ( input )
+}

tests/modules/picard/addorreplacereadgroups/nextflow.config

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

tests/modules/picard/addorreplacereadgroups/test.yml

@@ -0,0 +1,10 @@
+- name: picard addorreplacereadgroups test_picard_addorreplacereadgroups
+  command: nextflow run tests/modules/picard/addorreplacereadgroups -entry test_picard_addorreplacereadgroups -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/addorreplacereadgroups
+  files:
+    - path: output/picard/test.bam
+      md5sum: 7b82f3461c2d80fc6a10385e78c9427f
+    - path: output/picard/versions.yml
+      md5sum: 8a2d176295e1343146ea433c79bb517f

tests/modules/picard/cleansam/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CLEANSAM } from '../../../../modules/picard/cleansam/main.nf'
+
+workflow test_picard_cleansam {
+    
+    input = [ 
+        [ id:'test', single_end:true ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_CLEANSAM ( input )
+}

tests/modules/picard/cleansam/nextflow.config

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

tests/modules/picard/cleansam/test.yml

@@ -0,0 +1,10 @@
+- name: picard cleansam test_picard_cleansam
+  command: nextflow run tests/modules/picard/cleansam -entry test_picard_cleansam -c tests/config/nextflow.config
+  tags:
+    - picard/cleansam
+    - picard
+  files:
+    - path: output/picard/test.sam
+      md5sum: e314171a6060eb79947c13ad126ddf00
+    - path: output/picard/versions.yml
+      md5sum: e6457d7c6de51bf6f4b577eda65e57ac

tests/modules/picard/createsequencedictionary/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_CREATESEQUENCEDICTIONARY } from '../../../../modules/picard/createsequencedictionary/main.nf'
+
+workflow test_picard_createsequencedictionary {
+    
+    input = [ 
+        [ id:'test' ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) 
+    ]
+
+    PICARD_CREATESEQUENCEDICTIONARY ( input )
+}

tests/modules/picard/createsequencedictionary/nextflow.config

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

tests/modules/picard/createsequencedictionary/test.yml

@@ -0,0 +1,10 @@
+- name: picard createsequencedictionary test_picard_createsequencedictionary
+  command: nextflow run tests/modules/picard/createsequencedictionary -entry test_picard_createsequencedictionary -c tests/config/nextflow.config
+  tags:
+    - picard/createsequencedictionary
+    - picard
+  files:
+    - path: output/picard/test.dict
+      contains: ['SN:MT192765.1']
+    - path: output/picard/versions.yml
+      md5sum: b3d8c7ea65b8a6d3237b153d13fe2014

tests/modules/picard/fixmateinformation/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { PICARD_FIXMATEINFORMATION } from '../../../../modules/picard/fixmateinformation/main.nf'
+
+workflow test_picard_fixmateinformation {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) 
+    ]
+
+    PICARD_FIXMATEINFORMATION ( input )
+}

tests/modules/picard/fixmateinformation/nextflow.config

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

tests/modules/picard/fixmateinformation/test.yml

@@ -0,0 +1,10 @@
+- name: picard fixmateinformation test_picard_fixmateinformation
+  command: nextflow run tests/modules/picard/fixmateinformation -entry test_picard_fixmateinformation -c tests/config/nextflow.config
+  tags:
+    - picard
+    - picard/fixmateinformation
+  files:
+    - path: output/picard/test.bam
+      md5sum: 746102e8c242c0ef42e045c49d320030
+    - path: output/picard/versions.yml
+      md5sum: 4329ba7cdca8f4f6018dfd5c019ba2eb

tests/modules/rgi/main/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RGI_MAIN } from '../../../../modules/rgi/main/main.nf'
+
+workflow test_rgi_main {
+
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    RGI_MAIN ( input )
+}

tests/modules/rgi/main/nextflow.config

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

tests/modules/rgi/main/test.yml

@@ -0,0 +1,12 @@
+- name: rgi main
+  command: nextflow run ./tests/modules/rgi/main -entry test_rgi_main -c ./tests/config/nextflow.config -c ./tests/modules/rgi/main/nextflow.config
+  tags:
+    - rgi
+    - rgi/main
+  files:
+    - path: output/rgi/test.json
+      contains: ["NZ_LS483480", "orf_end", "perc_identity", "Pulvomycin"]
+    - path: output/rgi/test.txt
+      contains: ["NZ_LS483480", "ORF_ID", "Model_type", "Pulvomycin"]
+    - path: output/rgi/versions.yml
+      md5sum: 614a45d9d59680d4e743498773cf830a

tests/modules/sistr/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SISTR } from '../../../modules/sistr/main.nf'
+
+workflow test_sistr {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true) 
+    ]
+
+    SISTR ( input )
+}

tests/modules/sistr/nextflow.config

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

tests/modules/sistr/test.yml

@@ -0,0 +1,15 @@
+- name: sistr test_sistr
+  command: nextflow run tests/modules/sistr -entry test_sistr -c tests/config/nextflow.config
+  tags:
+    - sistr
+  files:
+    - path: output/sistr/test-allele.fasta
+      md5sum: 144a74999eb9dd01520be5c61e8bd210
+    - path: output/sistr/test-allele.json
+      md5sum: 3eb993c9489904621f539a93ff9a90ec
+    - path: output/sistr/test-cgmlst.csv
+      md5sum: c50a2144955fe1b98a6d5792bf295088
+    - path: output/sistr/test.tab
+      contains: ["cgmlst_ST", "serovar", "matched"]
+    - path: output/sistr/versions.yml
+      md5sum: 8b852f002c3ce67e3f6498da15b28296

tests/modules/vcfanno/main.nf

@@ -2,18 +2,40 @@
 
 nextflow.enable.dsl = 2
 
+include { UNTAR } from '../../../modules/untar/main.nf'
 include { VCFANNO } from '../../../modules/vcfanno/main.nf'
 
 workflow test_vcfanno {
     
     input = [ 
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test_compressed', single_end:false ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
         file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
     ]
+    
+    input_2 = [ [ id:'test_compressed', single_end:false ], // meta map 
+                [] ]
 
-    toml = file("https://raw.githubusercontent.com/nf-core/test-datasets/8fbd9f99a2feb3f9e39cd3bcdc4a9176a5835673/data/delete_me/vcfanno.toml", 
-                checkIfExists: true)
+    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+    resource_dir = file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true)
 
-    VCFANNO ( input, toml )
+    UNTAR ( resource_dir )
+    VCFANNO ( input, input_2, toml, UNTAR.out.untar )
 }
+
+workflow test_vcfanno_uncompressed {
+
+    input = [ [ id:'test_uncompressed', single_end:false ], // meta map
+                [] ,[] ]
+    
+    input_2 = [ 
+        [ id:'test_uncompressed', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+    ]
+
+    toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
+    resource_dir = file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true)
+
+    UNTAR ( resource_dir )
+    VCFANNO ( input, input_2, toml, UNTAR.out.untar )
+}

tests/modules/vcfanno/nextflow.config

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

tests/modules/vcfanno/test.yml

@@ -3,7 +3,21 @@
   tags:
     - vcfanno
   files:
-    - path: output/vcfanno/test_annotated.vcf
-      md5sum: 34259cf6b0a4698a2917ad3554b50c0f
+    - path: output/untar/versions.yml
+      md5sum: 6de038155bccbe4d264d09529bf9f4d8
+    - path: output/vcfanno/test_compressed_annotated.vcf
+      md5sum: 90ceb2fd2e06e781846d69c3981db665
     - path: output/vcfanno/versions.yml
       md5sum: 62d13540503b22f04a2280c91942cb03
+
+- name: vcfanno test_vcfanno_uncompressed
+  command: nextflow run tests/modules/vcfanno -entry test_vcfanno_uncompressed -c tests/config/nextflow.config
+  tags:
+    - vcfanno
+  files:
+    - path: output/untar/versions.yml
+      md5sum: a0de70274caac0cca31b077a1e7172d9
+    - path: output/vcfanno/test_uncompressed_annotated.vcf
+      md5sum: 90ceb2fd2e06e781846d69c3981db665
+    - path: output/vcfanno/versions.yml
+      md5sum: 300218dad68c3ffcc4783daa4f7c5a43