Merge branch 'nf-core:master' into master

README.md

@@ -133,7 +133,7 @@ We have written a helper command in the `nf-core/tools` package that uses the Gi
 
 ## Adding new modules
 
-If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/adding_modules).
+If you wish to contribute a new module, please see the documentation on the [nf-core website](https://nf-co.re/developers/modules#writing-a-new-module-reference).
 
 > Please be kind to our code reviewers and submit one pull request per module :)
 

modules/adapterremovalfixprefix/main.nf

@@ -0,0 +1,38 @@
+def VERSION = '0.05'
+
+process ADAPTERREMOVALFIXPREFIX {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
+        'quay.io/biocontainers/adapterremovalfixprefix:0.0.5--hdfd78af_2' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: fixed_fastq
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
+    """
+    AdapterRemovalFixPrefix \\
+        $fastq \\
+        $args \\
+        | gzip > ${prefix}.fq.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        adapterremovalfixprefix: $VERSION
+    END_VERSIONS
+    """
+}

modules/adapterremovalfixprefix/meta.yml

@@ -0,0 +1,43 @@
+name: adapterremovalfixprefix
+description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup.
+keywords:
+  - adapterremoval
+  - fastq
+  - dedup
+tools:
+  - adapterremovalfixprefix:
+      description: Fixes adapter removal prefixes to make sure no clashing read names are in the output.
+      homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix
+      documentation: None
+      tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix
+      doi: "10.1186/s13059-016-0918-z"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastq:
+      type: file
+      description: FASTQ file from AdapterRemoval2
+      pattern: "*.{fq.gz,fastq.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"
+  - fixed_fastq:
+      type: file
+      description: FASTQ file with fixed read prefixes for DeDup
+      pattern: "*.{fq.gz}"
+
+authors:
+  - "@jfy133"

modules/bracken/bracken/main.nf

@@ -0,0 +1,41 @@
+process BRACKEN_BRACKEN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bracken=2.6.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bracken:2.6.2--py39hc16433a_0':
+        'quay.io/biocontainers/bracken:2.6.2--py39hc16433a_0' }"
+
+    input:
+    tuple val(meta), path(kraken_report)
+    path database
+
+    output:
+    tuple val(meta), path(bracken_report), emit: reports
+    path "versions.yml"          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def threshold = meta.threshold ?: 10
+    def taxonomic_level = meta.taxonomic_level ?: 'S'
+    def read_length = meta.read_length ?: 150
+    def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def bracken_version = '2.6.2'
+    bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    """
+    bracken \\
+        ${args} \\
+        -d '${database}' \\
+        -i '${kraken_report}' \\
+        -o '${bracken_report}'
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bracken: ${bracken_version}
+    END_VERSIONS
+    """
+}

modules/bracken/bracken/meta.yml

@@ -0,0 +1,45 @@
+name: bracken_bracken
+description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
+keywords:
+  - sort
+tools:
+  - bracken:
+      description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
+      homepage: https://ccb.jhu.edu/software/bracken/
+      documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
+      tool_dev_url: https://github.com/jenniferlu717/Bracken
+      doi: "10.7717/peerj-cs.104"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - kraken_report:
+      type: file
+      description: TSV file with six columns coming from kraken2 output
+      pattern: "*.{tsv}"
+  - database:
+      type: file
+      description: Directory containing the kraken2/Bracken files for analysis
+      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"
+  - reports:
+      type: file
+      description: TSV output report of the re-estimated abundances
+      pattern: "*.{tsv}"
+
+authors:
+  - "@Midnighter"

modules/star/align/main.nf

@@ -29,6 +29,7 @@ process STAR_ALIGN {
     tuple val(meta), path('*fastq.gz')               , optional:true, emit: fastq
     tuple val(meta), path('*.tab')                   , optional:true, emit: tab
     tuple val(meta), path('*.out.junction')          , optional:true, emit: junction
+    tuple val(meta), path('*.out.sam')               , optional:true, emit: sam
 
     when:
     task.ext.when == null || task.ext.when

modules/svdb/merge/main.nf

@@ -2,10 +2,10 @@ process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcfs)

modules/svdb/query/main.nf

@@ -2,36 +2,73 @@ process SVDB_QUERY {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::svdb=2.5.0" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.5.0--py39hcbe4a3b_0':
+        'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.5.0--py39hcbe4a3b_0' }"
+        'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
 
     input:
     tuple val(meta), path(vcf)
-    path (vcf_db)
+    val(in_occs)
+    val(in_frqs)
+    val(out_occs)
+    val(out_frqs)
+    path (vcf_dbs)
 
     output:
-    tuple val(meta), path("*_ann_svdbq.vcf"), emit: vcf
+    tuple val(meta), path("*_query.vcf"), emit: vcf
     path "versions.yml"                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args    = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def in_occ  = ""
+    def in_frq  = ""
+    def out_occ = ""
+    def out_frq = ""
+    if (in_occs) {
+        in_occ  = "--in_occ ${in_occs.join(',')}"
+    }
+    if (in_frqs) {
+        in_frq  = "--in_frq ${in_frqs.join(',')}"
+    }
+    if (out_occs) {
+        out_occ = "--out_occ ${out_occs.join(',')}"
+    }
+    if (out_frqs) {
+        out_frq = "--out_frq ${out_frqs.join(',')}"
+    }
+
     """
     svdb \\
         --query \\
+        $in_occ \\
+        $in_frq \\
+        $out_occ \\
+        $out_frq \\
         $args \\
-        --db $vcf_db \\
+        --db ${vcf_dbs.join(',')} \\
         --query_vcf $vcf \\
-        >${prefix}_ann_svdbq.vcf
+        --prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_query.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' )
+    END_VERSIONS
+    """
+
 }

modules/svdb/query/meta.yml

@@ -15,6 +15,12 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - in_occs:
+      type: list
+      description: A list of allele count tags
+  - in_frqs:
+      type: list
+      description: A list of allele frequency tags
   - vcf:
       type: file
       description: query vcf file
@@ -34,10 +40,16 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
+  - out_occs:
+      type: list
+      description: A list of allele count tags
+  - out_frqs:
+      type: list
+      description: A list of allele frequency tags
   - vcf:
       type: file
       description: Annotated output VCF file
-      pattern: "*_ann_svdbq.vcf"
+      pattern: "*_query.vcf"
 
 authors:
   - "@ramprasadn"

modules/untar/main.nf

@@ -8,19 +8,19 @@ process UNTAR {
         'biocontainers/biocontainers:v1.2.0_cv1' }"
 
     input:
-    path archive
+    tuple val(meta), path(archive)
 
     output:
-    path "$untar"      , emit: untar
+    tuple val(meta), path("$untar"), emit: untar
-    path "versions.yml", emit: versions
+    path "versions.yml"            , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args  = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
-    untar        = archive.toString() - '.tar.gz'
+    untar     = archive.toString() - '.tar.gz'
     """
     tar \\
         -xzvf \\

modules/untar/meta.yml

@@ -10,11 +10,21 @@ tools:
       documentation: https://www.gnu.org/software/tar/manual/
       licence: ["GPL-3.0-or-later"]
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - archive:
       type: file
       description: File to be untar
       pattern: "*.{tar}.{gz}"
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - untar:
       type: file
       description:

modules/unzip/main.nf

@@ -8,11 +8,11 @@ process UNZIP {
         'quay.io/biocontainers/p7zip:15.09--h2d50403_4' }"
 
     input:
-    path archive
+    tuple val(meta), path(archive)
 
     output:
-    path "${archive.baseName}/", emit: unzipped_archive
+    tuple val(meta), path("${archive.baseName}/"), emit: unzipped_archive
-    path "versions.yml"        , emit: versions
+    path "versions.yml"                          , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

modules/unzip/meta.yml

@@ -12,12 +12,22 @@ tools:
       licence: ["LGPL-2.1-or-later"]
 
 input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - archive:
       type: file
       description: ZIP file
       pattern: "*.zip"
 
 output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - unzipped_archive:
       type: directory
       description: Directory contents of the unzipped archive

tests/config/pytest_modules.yml

@@ -14,6 +14,10 @@ adapterremoval:
   - modules/adapterremoval/**
   - tests/modules/adapterremoval/**
 
+adapterremovalfixprefix:
+  - modules/adapterremovalfixprefix/**
+  - tests/modules/adapterremovalfixprefix/**
+
 agrvate:
   - modules/agrvate/**
   - tests/modules/agrvate/**
@@ -309,6 +313,10 @@ bowtie2/build:
   - modules/bowtie2/build/**
   - tests/modules/bowtie2/build_test/**
 
+bracken/bracken:
+  - modules/bracken/bracken/**
+  - tests/modules/bracken/bracken/**
+
 bwa/aln:
   - modules/bwa/aln/**
   - tests/modules/bwa/aln/**

tests/config/test_data.config

@@ -25,6 +25,9 @@ params {
                 kraken2                                        = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
                 kraken2_tar_gz                                 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
 
+                kraken2_bracken                                = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken"
+                kraken2_bracken_tar_gz                         = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2_bracken.tar.gz"
+
                 ncbi_taxmap_zip                                = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip"
                 taxon_list_txt                                 = "${test_data_dir}/genomics/sarscov2/genome/db/maltextract/taxon_list.txt"
 
@@ -140,6 +143,7 @@ params {
                 syntheticvcf_short_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
                 syntheticvcf_short_score                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.score"
                 gnomad_r2_1_1_sv_vcf_gz                        = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1-sv.vcf.gz"
+                gnomad2_r2_1_1_sv_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD2.r2.1.1-sv.vcf.gz"
 
                 hapmap_3_3_hg38_21_vcf_gz                      = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz"
                 hapmap_3_3_hg38_21_vcf_gz_tbi                  = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/hapmap_3.3.hg38.vcf.gz.tbi"

tests/modules/adapterremovalfixprefix/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ADAPTERREMOVAL          } from '../../../modules/adapterremoval/main.nf'
+include { ADAPTERREMOVALFIXPREFIX } from '../../../modules/adapterremovalfixprefix/main.nf'
+
+workflow test_adapterremovalfixprefix {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    ADAPTERREMOVAL ( input, [] )
+    ADAPTERREMOVALFIXPREFIX ( ADAPTERREMOVAL.out.collapsed )
+}

tests/modules/adapterremovalfixprefix/nextflow.config

@@ -0,0 +1,9 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: ADAPTERREMOVAL {
+        ext.args = "--collapse"
+    }
+
+}

tests/modules/adapterremovalfixprefix/test.yml

@@ -0,0 +1,9 @@
+- name: adapterremovalfixprefix test_adapterremovalfixprefix
+  command: nextflow run tests/modules/adapterremovalfixprefix -entry test_adapterremovalfixprefix -c tests/config/nextflow.config
+  tags:
+    - adapterremovalfixprefix
+  files:
+    - path: output/adapterremovalfixprefix/test.fq.gz
+      md5sum: ff956de3532599a56c3efe5369f0953f
+    - path: output/adapterremovalfixprefix/versions.yml
+      md5sum: 983cb58079bf015c1d489a7e48261746

tests/modules/amps/main.nf

@@ -15,18 +15,21 @@ workflow test_amps {
     fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     gff = []
     seq_type = "DNA"
-    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
-    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
     mode = "BlastN"
     taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
-    ncbi_dir = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
-    filter = "def_anc"
 
     UNZIP_MALT ( map_db )
     UNZIP_MALTEXTRACT ( ncbi_dir )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
     MALT_RUN ( input, mode, MALT_BUILD.out.index )
-    MALTEXTRACT ( MALT_RUN.out.rma6, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive)
+    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
+    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
 
     AMPS ( MALTEXTRACT.out.results, taxon_list, filter )
 }

tests/modules/artic/minion/main.nf

@@ -11,12 +11,12 @@ workflow test_artic_minion {
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
     ]
-    fast5_tar          = file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true)
+    fast5_tar          = [ [], file(params.test_data['sarscov2']['nanopore']['fast5_tar_gz'], checkIfExists: true) ]
     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)
 
-    fast5_dir = UNTAR ( fast5_tar ).untar
+    fast5_dir = UNTAR ( fast5_tar ).untar.map{ it[1] }
 
     ARTIC_MINION ( input, fast5_dir, sequencing_summary, fasta, bed, [], '', 'nCoV-2019', '3')
 }

tests/modules/bracken/bracken/main.nf

@@ -0,0 +1,57 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UNTAR           } from '../../../../modules/untar/main.nf'
+include { KRAKEN2_KRAKEN2 } from '../../../../modules/kraken2/kraken2/main.nf'
+include { BRACKEN_BRACKEN } from '../../../../modules/bracken/bracken/main.nf'
+
+workflow test_bracken_bracken_single_end_default_args {
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_single_end_custom_args {
+    input = [ [ id:'test', single_end:true, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_default_args {
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}
+
+workflow test_bracken_bracken_paired_end_custom_args {
+    input = [ [ id:'test', single_end:false, threshold:0, taxonomic_level:'G', read_length:100 ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
+            ]
+    db    = file(params.test_data['sarscov2']['genome']['kraken2_bracken_tar_gz'], checkIfExists: true)
+
+    ch_db = UNTAR ( [[:], db] ).untar
+        .map { it[1] }
+    KRAKEN2_KRAKEN2 ( input, ch_db )
+    BRACKEN_BRACKEN ( KRAKEN2_KRAKEN2.out.txt, ch_db )
+}

tests/modules/bracken/bracken/nextflow.config

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

tests/modules/bracken/bracken/test.yml

@@ -0,0 +1,43 @@
+- name: bracken bracken test_bracken_bracken_single_end_default_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_default_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: ab8b1550f84a99bae80f050fe718abd0
+
+- name: bracken bracken test_bracken_bracken_single_end_custom_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_single_end_custom_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: af87e8d4c42fbcb0469ab13912b8a9bd
+
+- name: bracken bracken test_bracken_bracken_paired_end_default_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_default_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_S.tsv
+      md5sum: 4a21ae14ff8a0311d55f139af5247838
+    - path: output/bracken/versions.yml
+      md5sum: 4602111eb25bd19a7f9d725acc5921f6
+
+- name: bracken bracken test_bracken_bracken_paired_end_custom_args
+  command: nextflow run tests/modules/bracken/bracken -entry test_bracken_bracken_paired_end_custom_args -c tests/config/nextflow.config
+  tags:
+    - bracken/bracken
+    - bracken
+  files:
+    - path: output/bracken/test_G.tsv
+      md5sum: f609b09d6edb5ebc1ea1435d1dd46cde
+    - path: output/bracken/versions.yml
+      md5sum: d4618b01df5ac09cc366fe2ae7c13f06

tests/modules/cellranger/mkfastq/main.nf

@@ -8,19 +8,19 @@ include { CELLRANGER_MKFASTQ } from '../../../../modules/cellranger/mkfastq/main
 workflow test_cellranger_mkfastq_simple {
 
     simple_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-simple-1.2.0.csv", checkIfExists: true)
-    tiny_bcl = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true)
+    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
 
     UNTAR ( tiny_bcl )
 
-    CELLRANGER_MKFASTQ ( UNTAR.out.untar, simple_csv)
+    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, simple_csv)
 }
 
 workflow test_cellranger_mkfastq_illumina {
 
     samplesheet_csv = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-samplesheet-1.2.0.csv", checkIfExists: true)
-    tiny_bcl = file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true)
+    tiny_bcl = [ [], file("https://cf.10xgenomics.com/supp/cell-exp/cellranger-tiny-bcl-1.2.0.tar.gz", checkIfExists: true) ]
 
     UNTAR ( tiny_bcl )
 
-    CELLRANGER_MKFASTQ ( UNTAR.out.untar, samplesheet_csv)
+    CELLRANGER_MKFASTQ ( UNTAR.out.untar.map{ it[1] }, samplesheet_csv)
 }

tests/modules/controlfreec/main.nf

@@ -19,7 +19,7 @@ workflow test_controlfreec {
     dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
     dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
 
-    chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
+    chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
     target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
 
     UNTAR(chrfiles)
@@ -29,7 +29,7 @@ workflow test_controlfreec {
                             [],
                             dbsnp,
                             dbsnp_tbi,
-                            UNTAR.out.untar,
+                            UNTAR.out.untar.map{ it[1] },
                             [],
                             target_bed,
                             []

tests/modules/gatk4/createsomaticpanelofnormals/main.nf

@@ -6,12 +6,12 @@ include { UNTAR           } from '../../../../modules/untar/main.nf'
 include { GATK4_CREATESOMATICPANELOFNORMALS } from '../../../../modules/gatk4/createsomaticpanelofnormals/main.nf'
 
 workflow test_gatk4_createsomaticpanelofnormals {
-    db    = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    db    = [[], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
 
     input = Channel.of([ id:'test'])
-              .combine(UNTAR.out.untar)
+              .combine(UNTAR.out.untar.map{ it[1] })
 
     fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
     fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)

tests/modules/gatk4/genomicsdbimport/main.nf

@@ -22,7 +22,7 @@ workflow test_gatk4_genomicsdbimport_create_genomicsdb {
 }
 
 workflow test_gatk4_genomicsdbimport_get_intervalslist {
-    db    = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
 
@@ -31,7 +31,7 @@ workflow test_gatk4_genomicsdbimport_get_intervalslist {
               [] ,
               [] ,
               [] ])
-              .combine(UNTAR.out.untar)
+              .combine(UNTAR.out.untar.map{ it[1] })
 
     run_intlist = true
     run_updatewspace = false
@@ -41,7 +41,7 @@ workflow test_gatk4_genomicsdbimport_get_intervalslist {
 }
 
 workflow test_gatk4_genomicsdbimport_update_genomicsdb {
-    db    = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    db    = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
 
@@ -50,7 +50,7 @@ workflow test_gatk4_genomicsdbimport_update_genomicsdb {
               file( params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz_tbi'] , checkIfExists: true) ,
               [] ,
               [] ])
-              .combine(UNTAR.out.untar)
+              .combine(UNTAR.out.untar.map{ it[1] })
 
     run_intlist = false
     run_updatewspace = true

tests/modules/gatk4/genotypegvcfs/main.nf

@@ -97,10 +97,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
     fastaIndex      = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     fastaDict       = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
-    test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.collect()
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([])
 
@@ -119,10 +119,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
     dbsnp        = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
     dbsnpIndex   = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
 
-    test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.collect()
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([])
     input = Channel.of([ id:'test' ]).combine(gendb)
@@ -137,10 +137,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
     fastaIndex   = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
     fastaDict    = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
 
-    test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.collect()
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
     input = Channel.of([ id:'test' ]).combine(gendb)
@@ -158,10 +158,10 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
     dbsnp        = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
     dbsnpIndex   = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
 
-    test_genomicsdb = file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true)
+    test_genomicsdb = [ [], file(params.test_data['homo_sapiens']['illumina']['test_genomicsdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( test_genomicsdb )
-    gendb = UNTAR.out.untar.collect()
+    gendb = UNTAR.out.untar.map{ it[1] }.collect()
     gendb.add([])
     gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
     input = Channel.of([ id:'test' ]).combine(gendb)

tests/modules/kraken2/kraken2/main.nf

@@ -9,10 +9,10 @@ workflow test_kraken2_kraken2_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar )
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_kraken2_kraken2_paired_end {
@@ -20,8 +20,8 @@ workflow test_kraken2_kraken2_paired_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    db    = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
+    db    = [ [], file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
-    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar )   
+    KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] } )
 }

tests/modules/last/lastal/main.nf

@@ -10,10 +10,10 @@ workflow test_last_lastal_with_dummy_param_file {
     input = [ [ id:'contigs', single_end:false ], // meta map
               file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
               [] ]
-    db    = [ file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+    db    = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
-    LAST_LASTAL ( input, UNTAR.out.untar)
+    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
 }
 
 workflow test_last_lastal_with_real_param_file {
@@ -21,8 +21,8 @@ workflow test_last_lastal_with_real_param_file {
     input      = [ [ id:'contigs', single_end:false ], // meta map
                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
                    file(params.test_data['sarscov2']['genome']['contigs_genome_par'], checkIfExists: true) ]
-    db         = [ file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+    db         = [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( db )
-    LAST_LASTAL ( input, UNTAR.out.untar)
+    LAST_LASTAL ( input, UNTAR.out.untar.map{ it[1] })
 }

tests/modules/last/train/main.nf

@@ -7,9 +7,9 @@ include { LAST_TRAIN } from '../../../../modules/last/train/main.nf'
 
 workflow test_last_train {
 
-    db =         [ file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
+    db =         [ [], file(params.test_data['sarscov2']['genome']['lastdb_tar_gz'], checkIfExists: true) ]
     input =      [ [ id:'contigs' ], // meta map
                    file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
     UNTAR ( db )
-    LAST_TRAIN ( input, UNTAR.out.untar )
+    LAST_TRAIN ( input, UNTAR.out.untar.map{ it[1] } )
 }

tests/modules/malt/build_test/main.nf

@@ -9,18 +9,18 @@ workflow test_malt_build {
     fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     seq_type = "DNA"
     gff = []
-    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
 
     UNZIP ( map_db )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map{ it[1] } )
 }
 
 workflow test_malt_build_gff {
     fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     seq_type = "DNA"
     gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
-    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
 
     UNZIP ( map_db )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map{ it[1] } )
 }

tests/modules/malt/run/main.nf

@@ -2,16 +2,16 @@
 
 nextflow.enable.dsl = 2
 
-include { UNZIP } from '../../../../modules/unzip/main.nf'
+include { UNZIP      } from '../../../../modules/unzip/main.nf'
 include { MALT_BUILD } from  '../../../../modules/malt/build/main.nf'
-include { MALT_RUN } from '../../../../modules/malt/run/main.nf'
+include { MALT_RUN   } from '../../../../modules/malt/run/main.nf'
 
 workflow test_malt_run {
 
     fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
     seq_type = "DNA"
-    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
@@ -19,7 +19,7 @@ workflow test_malt_run {
     mode = "BlastN"
 
     UNZIP ( map_db )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP.out.unzipped_archive.map { it[1] } )
     MALT_RUN ( input, mode, MALT_BUILD.out.index )
 }
 

tests/modules/maltextract/main.nf

@@ -4,24 +4,28 @@ nextflow.enable.dsl = 2
 
 include { UNZIP as UNZIP_MALT        } from '../../../modules/unzip/main.nf'
 include { UNZIP as UNZIP_MALTEXTRACT }  from '../../../modules/unzip/main.nf'
-include { MALT_BUILD  } from  '../../../modules/malt/build/main.nf'
+include { MALT_BUILD                 } from  '../../../modules/malt/build/main.nf'
-include { MALT_RUN    } from '../../../modules/malt/run/main.nf'
+include { MALT_RUN                   } from '../../../modules/malt/run/main.nf'
-include { MALTEXTRACT } from '../../../modules/maltextract/main.nf'
+include { MALTEXTRACT                } from '../../../modules/maltextract/main.nf'
 
 workflow test_maltextract {
 
     fastas = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     gff = []
     seq_type = "DNA"
-    map_db = file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true)
+    map_db = [ [], file("https://software-ab.informatik.uni-tuebingen.de/download/megan6/megan-nucl-Jan2021.db.zip", checkIfExists: true) ]
-    input = file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+    ]
     mode = "BlastN"
     taxon_list = file(params.test_data['sarscov2']['genome']['taxon_list_txt'], checkIfExists: true)
-    ncbi_dir = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    ncbi_dir = [ [], file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true) ]
 
     UNZIP_MALT ( map_db )
     UNZIP_MALTEXTRACT ( ncbi_dir )
-    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive )
+    MALT_BUILD ( fastas, seq_type, gff, UNZIP_MALT.out.unzipped_archive.map{ it[1] } )
     MALT_RUN ( input, mode, MALT_BUILD.out.index )
-    MALTEXTRACT ( MALT_RUN.out.rma6, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive)
+    ch_input_to_maltextract = MALT_RUN.out.rma6.map{ it[1] }
+    MALTEXTRACT ( ch_input_to_maltextract, taxon_list, UNZIP_MALTEXTRACT.out.unzipped_archive.map{ it[1] })
 }

tests/modules/maltextract/test.yml

@@ -3,8 +3,6 @@
   tags:
     - maltextract
   files:
-    - path: output/maltextract/results/error.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/maltextract/results/error.txt
     - path: output/maltextract/results/log.txt
       contains:

tests/modules/metaphlan3/main.nf

@@ -12,10 +12,10 @@ workflow test_metaphlan3_single_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
             ]
 
-    db    = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar )
+    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_paired_end {
@@ -25,11 +25,10 @@ workflow test_metaphlan3_paired_end {
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
 
-    db    = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar )
+    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_sam {
@@ -38,12 +37,11 @@ workflow test_metaphlan3_sam {
               [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
             ]
 
-    db    = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
-
 
     UNTAR ( db )
     SAMTOOLS_VIEW ( input, [] )
-    METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar )
+    METAPHLAN3 ( SAMTOOLS_VIEW.out.bam, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_metaphlan3_fasta {
@@ -52,8 +50,8 @@ workflow test_metaphlan3_fasta {
               [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
             ]
 
-    db    = channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', type: 'dir', checkIfExists: true)
+    db    = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/metaphlan_database.tar.gz', checkIfExists: true) ]
 
     UNTAR ( db )
-    METAPHLAN3 ( input, UNTAR.out.untar )
+    METAPHLAN3 ( input, UNTAR.out.untar.map{ it[1] } )
 }

tests/modules/sratools/fasterqdump/main.nf

@@ -7,22 +7,22 @@ include { SRATOOLS_FASTERQDUMP } from '../../../../modules/sratools/fasterqdump/
 
 workflow test_sratools_fasterqdump_single_end {
 
-    archive = file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true)
+    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR13255544_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
 
     def input = Channel.of([ id:'test_single_end', single_end:true ])
-        .combine(UNTAR.out.untar)
+        .combine(UNTAR.out.untar.map{ it[1] })
 
     SRATOOLS_FASTERQDUMP ( input )
 }
 
 workflow test_sratools_fasterqdump_paired_end {
 
-    archive = file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true)
+    archive = [ [], file(params.test_data['sarscov2']['illumina']['SRR11140744_tar_gz'], checkIfExists: true) ]
     UNTAR ( archive )
 
     def input = Channel.of([ id:'test_paired_end', single_end:false ])
-        .combine(UNTAR.out.untar)
+        .combine(UNTAR.out.untar.map{ it[1] })
 
     SRATOOLS_FASTERQDUMP ( input )
 }

tests/modules/svdb/query/main.nf

@@ -14,5 +14,29 @@ workflow test_svdb_query {
                 file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true)
             ]
 
-    SVDB_QUERY ( input, vcf_db )
+    in_occs = ['AC']
+    in_frqs = ['AF']
+    out_occs = ['gnomad_svAC']
+    out_frqs = ['gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
+}
+
+workflow test_svdb_query_multiple {
+
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_sv_vcf'], checkIfExists: true) ]
+            ]
+
+    vcf_db = [
+                file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_sv_vcf_gz'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['genome']['gnomad2_r2_1_1_sv_vcf_gz'], checkIfExists: true)
+            ]
+
+    in_occs = ['AC','AC']
+    in_frqs = ['AF','AF']
+    out_occs = ['gnomad_svAC','gnomad_svAC']
+    out_frqs = ['gnomad_svAF','gnomad_svAF']
+
+    SVDB_QUERY ( input, in_occs, in_frqs, out_occs, out_frqs, vcf_db )
 }

tests/modules/svdb/query/nextflow.config

@@ -2,8 +2,4 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
-    withName: SVDB_QUERY {
-         ext.args = '--in_occ AC --out_occ gnomad_svAC --in_frq AF --out_frq gnomad_svAF'
-     }
-
 }

tests/modules/svdb/query/test.yml

@@ -4,4 +4,12 @@
     - svdb
     - svdb/query
   files:
-    - path: output/svdb/test_ann_svdbq.vcf
+    - path: output/svdb/test_query.vcf
+
+- name: svdb query multiple
+  command: nextflow run ./tests/modules/svdb/query -entry test_svdb_query_multiple -c ./tests/config/nextflow.config -c ./tests/modules/svdb/query/nextflow.config
+  tags:
+    - svdb
+    - svdb/query
+  files:
+    - path: output/svdb/test_query.vcf

tests/modules/untar/main.nf

@@ -5,7 +5,10 @@ nextflow.enable.dsl = 2
 include { UNTAR } from '../../../modules/untar/main.nf'
 
 workflow test_untar {
-    input = file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
+    input = [
+        [],
+        file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true)
+    ]
 
     UNTAR ( input )
 }

tests/modules/unzip/main.nf

@@ -6,7 +6,10 @@ include { UNZIP } from '../../../modules/unzip/main.nf'
 
 workflow test_unzip {
 
-    archive = file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    archive = [
+        [],
+        file(params.test_data['sarscov2']['genome']['ncbi_taxmap_zip'], checkIfExists: true)
+    ]
 
     UNZIP ( archive )
 }

tests/modules/vcfanno/main.nf

@@ -17,10 +17,10 @@ workflow test_vcfanno {
                 [] ]
 
     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)
+    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 )
+    VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_vcfanno_uncompressed {
@@ -34,8 +34,8 @@ workflow test_vcfanno_uncompressed {
     ]
 
     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)
+    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 )
+    VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
 }