Merge branch 'master' into new-module/EMBOSS_SEQRET

modules/busco/main.nf

@@ -9,7 +9,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path('tmp_input/*')
-    each lineage                          // Required:    lineage to check against, "auto" enables --auto-lineage instead
+    val lineage                           // Required:    lineage to check against, "auto" enables --auto-lineage instead
     path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
     path config_file                      // Optional:    busco configuration file
 

modules/checkm/lineagewf/main.nf

@@ -14,7 +14,8 @@ process CHECKM_LINEAGEWF {
 
     output:
     tuple val(meta), path("${prefix}")           , emit: checkm_output
-    tuple val(meta), path("${prefix}.tsv"), emit: checkm_tsv
+    tuple val(meta), path("${prefix}/lineage.ms"), emit: marker_file
+    tuple val(meta), path("${prefix}.tsv")       , emit: checkm_tsv
     path "versions.yml"                          , emit: versions
 
     when:

modules/checkm/lineagewf/meta.yml

@@ -52,6 +52,10 @@ output:
       type: directory
       description: CheckM output directory
       pattern: "*/"
+  - checkm_output:
+      type: file
+      description: Lineage markfer file
+      pattern: "lineage.ms"
   - checkm_tsv:
       type: file
       description: CheckM summary completeness statistics table

modules/checkm/qa/main.nf

@@ -0,0 +1,44 @@
+process CHECKM_QA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(analysis_dir), path(marker_file), path(coverage_file)
+    path exclude_marker_file
+
+    output:
+    tuple val(meta), path("${prefix}.txt")  , optional: true, emit: output
+    tuple val(meta), path("${prefix}.fasta"), optional: true, emit: fasta
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args     = task.ext.args ?: ''
+    prefix       = task.ext.prefix ?: "${meta.id}"
+    suffix       = task.ext.args?.matches(".*-o 9.*|.*--out_file 9.*") ? "fasta" : "txt"
+    def coverage = coverage_file                                   ? "--coverage_file ${coverage_file}"  : ""
+    def exclude  = exclude_marker_file                             ? "--exclude_markers ${marker_filer}" : ""
+    """
+    checkm \\
+        qa \\
+        --threads ${task.cpus} \\
+        --file ${prefix}.${suffix} \\
+        $marker_file \\
+        $analysis_dir \\
+        $coverage \\
+        $exclude \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        checkm: \$( checkm 2>&1 | grep '...:::' | sed 's/.*CheckM v//;s/ .*//' )
+    END_VERSIONS
+    """
+}

modules/checkm/qa/meta.yml

@@ -0,0 +1,67 @@
+name: checkm_qa
+description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
+keywords:
+  - checkm
+  - mag
+  - metagenome
+  - quality
+  - isolates
+  - microbes
+  - single cells
+  - completeness
+  - contamination
+  - bins
+  - genome bins
+  - qa
+  - quality assurnce
+tools:
+  - checkm:
+      description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
+      homepage: https://ecogenomics.github.io/CheckM/
+      documentation: https://github.com/Ecogenomics/CheckM/wiki
+      tool_dev_url: https://github.com/Ecogenomics/CheckM
+      doi: "10.1101/gr.186072.114"
+      licence: ["GPL v3"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - analysis_dir:
+      type: file
+      description: Directory containing output of checkm/analyze or checkm/lineage_wf etc.
+      pattern: "*"
+  - marker_file:
+      type: file
+      description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf
+      pattern: "*.ms"
+  - coverage_file:
+      type: file
+      description: File containing coverage of each sequence (generated by checkm coverage)
+  - exclude_marker_file:
+      type: file
+      description: File specifying markers to exclude from marker sets
+
+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"
+  - output:
+      type: file
+      description: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)"
+      pattern: "*.txt"
+  - fasta:
+      type: file
+      description: Output in fasta format (only if --out_format 9)
+      pattern: "*.fasta"
+
+authors:
+  - "@jfy133"

modules/fcs/fcsadaptor/main.nf

@@ -0,0 +1,49 @@
+process FCS_FCSADAPTOR {
+    tag "$meta.id"
+    label 'process_low'
+
+    if (params.enable_conda) {
+        exit 1, "Conda environments cannot be used when using the FCS tool. Please use docker or singularity containers."
+    }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/releases/0.2.3/fcs-adaptor.0.2.3.sif':
+        'ncbi/fcs-adaptor:0.2.3' }"
+
+    input:
+    tuple val(meta), path(assembly)
+
+    output:
+    tuple val(meta), path("*.cleaned_sequences.fa.gz"), emit: cleaned_assembly
+    tuple val(meta), path("*.fcs_adaptor_report.txt") , emit: adaptor_report
+    tuple val(meta), path("*.fcs_adaptor.log")        , emit: log
+    tuple val(meta), path("*.pipeline_args.yaml")     , emit: pipeline_args
+    tuple val(meta), path("*.skipped_trims.jsonl")    , emit: skipped_trims
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: '--prok' // --prok || --euk
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def FCSADAPTOR_VERSION = '0.2.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    /app/fcs/bin/av_screen_x \\
+        -o output/ \\
+        $args \\
+        $assembly
+
+    # compress and/or rename files with prefix
+    gzip -cf output/cleaned_sequences/* > "${prefix}.cleaned_sequences.fa.gz"
+    cp "output/fcs_adaptor_report.txt"    "${prefix}.fcs_adaptor_report.txt"
+    cp "output/fcs_adaptor.log"           "${prefix}.fcs_adaptor.log"
+    cp "output/pipeline_args.yaml"        "${prefix}.pipeline_args.yaml"
+    cp "output/skipped_trims.jsonl"       "${prefix}.skipped_trims.jsonl"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        FCS-adaptor: $FCSADAPTOR_VERSION
+    END_VERSIONS
+    """
+}

modules/fcs/fcsadaptor/meta.yml

@@ -0,0 +1,62 @@
+name: "fcs_fcsadaptor"
+description: Run NCBI's FCS adaptor on assembled genomes
+keywords:
+  - assembly
+  - genomics
+  - quality control
+  - contamination
+  - NCBI
+tools:
+  - "fcs":
+      description: |
+        The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign
+        organisms in genome assemblies to prepare your data for submission. Therefore, the
+        submission process to NCBI is faster and fewer contaminated genomes are submitted.
+        This reduces errors in analyses and conclusions, not just for the original data submitter
+        but for all subsequent users of the assembly.
+      homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/"
+      documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor"
+      tool_dev_url: "https://github.com/ncbi/fcs"
+      doi: ""
+      licence: "United States Government Work"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - assembly:
+      type: file
+      description: assembly fasta file
+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"
+  - cleaned_assembly:
+      type: file
+      description: Cleaned assembly in fasta format
+      pattern: "*.{cleaned_sequences.fa.gz}"
+  - adaptor_report:
+      type: file
+      description: Report of identified adaptors
+      pattern: "*.{fcs_adaptor_report.txt}"
+  - log:
+      type: file
+      description: Log file
+      pattern: "*.{fcs_adaptor.log}"
+  - pipeline_args:
+      type: file
+      description: Run arguments
+      pattern: "*.{pipeline_args.yaml}"
+  - skipped_trims:
+      type: file
+      description: Skipped trim information
+      pattern: "*.{skipped_trims.jsonl}"
+authors:
+  - "@d4straub"

modules/hisat2/align/main.nf

@@ -3,10 +3,10 @@ process HISAT2_ALIGN {
     label 'process_high'
 
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
-    conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.15.1" : null)
+    conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' :
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' :
-        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' }"
+        'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -25,7 +25,7 @@ process HISAT2_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {

modules/hisat2/build/main.nf

@@ -44,7 +44,7 @@ process HISAT2_BUILD {
         log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
         log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
     }
-    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     mkdir hisat2
     $extract_exons

modules/hisat2/extractsplicesites/main.nf

@@ -20,7 +20,7 @@ process HISAT2_EXTRACTSPLICESITES {
 
     script:
     def args = task.ext.args ?: ''
-    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
     cat <<-END_VERSIONS > versions.yml

modules/tabix/bgzip/main.nf

@@ -11,8 +11,8 @@ process TABIX_BGZIP {
     tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("${prefix}*"), emit: output
+    tuple val(meta), path("${output}")    , emit: output
-    tuple val(meta), path("*gzi")      , emit: gzi, optional: true
+    tuple val(meta), path("${output}.gzi"), emit: gzi, optional: true
     path  "versions.yml"                  , emit: versions
 
     when:
@@ -21,12 +21,13 @@ process TABIX_BGZIP {
     script:
     def args = task.ext.args ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-    in_bgzip = input.toString().endsWith(".gz")
+    in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
+    output   = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz"
     command1 = in_bgzip ? '-d' : '-c'
-    command2 = in_bgzip ? ''   : " > ${prefix}.${input.getExtension()}.gz"
+    command2 = in_bgzip ? ''   : " > ${output}"
     // Name the index according to $prefix, unless a name has been requested
     if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) {
-        args = args + " -I ${prefix}.${input.getExtension()}.gz.gzi"
+        args = args + " -I ${output}.gzi"
     }
     """
     bgzip $command1 $args -@${task.cpus} $input $command2

modules/vcflib/vcfbreakmulti/main.nf

@@ -0,0 +1,49 @@
+process VCFLIB_VCFBREAKMULTI {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::vcflib=1.0.3" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/vcflib:1.0.3--hecb563c_1':
+        'quay.io/biocontainers/vcflib:1.0.3--ha025227_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+
+    output:
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
+    path "versions.yml"              , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.0.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+
+    """
+    vcfbreakmulti \\
+        $vcf \\
+        $args \\
+        | bgzip -c $args2 > ${prefix}.breakmulti.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcflib: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.0.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.breakmulti.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        vcflib: $VERSION
+    END_VERSIONS
+    """
+}

modules/vcflib/vcfbreakmulti/meta.yml

@@ -0,0 +1,45 @@
+name: "vcflib_vcfbreakmulti"
+description: If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields
+keywords:
+  - vcflib
+  - vcflib/vcfbreakmulti
+tools:
+  - "vcflib":
+      description: "Command-line tools for manipulating VCF files"
+      homepage: https://github.com/vcflib/vcflib
+      documentation: https://github.com/vcflib/vcflib#USAGE
+      doi: "https://doi.org/10.1101/2021.05.21.445151"
+      licence: "['MIT']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.{.vcf.gz,vcf}"
+  - tbi:
+      type: file
+      description: Index of VCF file
+      pattern: "*.vcf.gz.tbi"
+
+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"
+  - vcf:
+      type: file
+      description: Compressed VCF file
+      pattern: "*.vcf.gz"
+
+authors:
+  - "@lucpen"

tests/config/pytest_modules.yml

@@ -499,6 +499,10 @@ checkm/lineagewf:
   - modules/checkm/lineagewf/**
   - tests/modules/checkm/lineagewf/**
 
+checkm/qa:
+  - modules/checkm/qa/**
+  - tests/modules/checkm/qa/**
+
 chromap/chromap:
   - modules/chromap/chromap/**
   - tests/modules/chromap/chromap/**
@@ -803,6 +807,10 @@ fasttree:
   - modules/fasttree/**
   - tests/modules/fasttree/**
 
+fcs/fcsadaptor:
+  - modules/fcs/fcsadaptor/**
+  - tests/modules/fcs/fcsadaptor/**
+
 ffq:
   - modules/ffq/**
   - tests/modules/ffq/**
@@ -2500,6 +2508,10 @@ vcfanno:
   - modules/vcfanno/**
   - tests/modules/vcfanno/**
 
+vcflib/vcfbreakmulti:
+  - modules/vcflib/vcfbreakmulti/**
+  - tests/modules/vcflib/vcfbreakmulti/**
+
 vcflib/vcfuniq:
   - modules/vcflib/vcfuniq/**
   - tests/modules/vcflib/vcfuniq/**

tests/modules/busco/main.nf

@@ -13,58 +13,11 @@ workflow test_busco_genome_single_fasta {
 
     BUSCO (
         input,
-        ['bacteria_odb10', 'bacteroidetes_odb10'],  // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
+        'bacteria_odb10', // Launch with 'auto' to use --auto-lineage, and specified lineages // 'auto' removed from test due to memory issues
         [], // Download busco lineage
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmpyz_hi62i/busco/
-    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/short_summary.specific.bacteria_odb10.genome.fna.txt
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.json
-    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco/
-    │   ├── genome.fna/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteria_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/33/7d8c9b2c8931d9ad6a67aa843895e7/test-bacteria_odb10-busco.batch_summary.txt
-    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco/
-    │   ├── genome.fna/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteroidetes_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-bacteroidetes_odb10-busco.batch_summary.txt -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/test-bacteroidetes_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpza_0dth3/6a/e95a0cd21785ce33d63b8f73a68a51/versions.yml
-    */
-
 }
 
 workflow test_busco_genome_multi_fasta {
@@ -84,49 +37,6 @@ workflow test_busco_genome_multi_fasta {
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmpk19byek7/busco/
-    ├── short_summary.specific.bacteria_odb10.genome.fasta.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.json
-    ├── short_summary.specific.bacteria_odb10.genome.fasta.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fasta.txt
-    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.json
-    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/short_summary.specific.bacteria_odb10.genome.fna.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco/
-    │   ├── genome.fasta/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteria_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   ├── genome.fna/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── prodigal_err.log
-    │   │   │   └── prodigal_out.log
-    │   │   ├── prodigal_output/
-    │   │   │   └── predicted_genes/
-    │   │   └── run_bacteria_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/test-bacteria_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmplt9fv3tl/15/ff310a16d9ce7ad24e207a05ce718e/versions.yml
-    */
-
 }
 
 workflow test_busco_eukaryote_metaeuk {
@@ -143,31 +53,6 @@ workflow test_busco_eukaryote_metaeuk {
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmpeq4dsir5/busco/
-    ├── short_summary.specific.eukaryota_odb10.genome.fasta.json -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.json
-    ├── short_summary.specific.eukaryota_odb10.genome.fasta.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/short_summary.specific.eukaryota_odb10.genome.fasta.txt
-    ├── test-eukaryota_odb10-busco -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco/
-    │   ├── genome.fasta/
-    │   │   ├── logs/
-    │   │   │   ├── hmmsearch_err.log
-    │   │   │   ├── hmmsearch_out.log
-    │   │   │   ├── metaeuk_err.log
-    │   │   │   └── metaeuk_out.log
-    │   │   └── run_eukaryota_odb10/
-    │   │       ├── busco_sequences/
-    │   │       ├── full_table.tsv
-    │   │       ├── hmmer_output/
-    │   │       ├── metaeuk_output/
-    │   │       ├── missing_busco_list.tsv
-    │   │       ├── short_summary.json
-    │   │       └── short_summary.txt
-    │   └── logs/
-    │       └── busco.log
-    ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/test-eukaryota_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmp60hby2pk/6f/529873d91cda6bae3a4a6a21746aee/versions.yml
-    */
-
 }
 
 workflow test_busco_eukaryote_augustus {
@@ -184,34 +69,6 @@ workflow test_busco_eukaryote_augustus {
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmp2xqaygjj/busco/
-    ├── test-eukaryota_odb10-busco -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco/
-    │   ├── genome.fasta/
-    │   │   ├── blast_db/
-    │   │   │   ├── genome.fasta.ndb
-    │   │   │   ├── genome.fasta.nhr
-    │   │   │   ├── genome.fasta.nin
-    │   │   │   ├── genome.fasta.not
-    │   │   │   ├── genome.fasta.nsq
-    │   │   │   ├── genome.fasta.ntf
-    │   │   │   └── genome.fasta.nto
-    │   │   ├── logs/
-    │   │   │   ├── makeblastdb_err.log
-    │   │   │   ├── makeblastdb_out.log
-    │   │   │   ├── tblastn_err.log
-    │   │   │   └── tblastn_out.log
-    │   │   └── run_eukaryota_odb10/
-    │   │       ├── augustus_output/
-    │   │       ├── blast_output/
-    │   │       ├── busco_sequences/
-    │   │       └── hmmer_output/
-    │   └── logs/
-    │       └── busco.log
-    ├── test-eukaryota_odb10-busco.batch_summary.txt -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/test-eukaryota_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpjqs61x9o/3f/67cc14e873c0ceb45e2a27594d624c/versions.yml
-    */
-
 }
 
 workflow test_busco_protein {
@@ -228,28 +85,8 @@ workflow test_busco_protein {
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmpzwd5dn56/busco/
-    ├── short_summary.specific.bacteria_odb10.proteome.fasta.json -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.json
-    ├── short_summary.specific.bacteria_odb10.proteome.fasta.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/short_summary.specific.bacteria_odb10.proteome.fasta.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco/
-    │   ├── logs/
-    │   │   └── busco.log
-    │   └── proteome.fasta/
-    │       ├── logs/
-    │       │   ├── hmmsearch_err.log
-    │       │   └── hmmsearch_out.log
-    │       └── run_bacteria_odb10/
-    │           ├── busco_sequences/
-    │           ├── full_table.tsv
-    │           ├── hmmer_output/
-    │           ├── missing_busco_list.tsv
-    │           ├── short_summary.json
-    │           └── short_summary.txt
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/test-bacteria_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmpk1nlgbf_/ae/0db07b5cd08fb23d0aba5f134ebbe2/versions.yml
-    */
 }
+
 workflow test_busco_transcriptome {
 
     input = [
@@ -264,63 +101,4 @@ workflow test_busco_transcriptome {
         [] // No config
     )
 
-    /* Output tree:
-    /tmp/tmpitjyvo9g/busco/
-    ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.json -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
-    ├── short_summary.specific.bacteria_odb10.test1.contigs.fa.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/short_summary.specific.bacteria_odb10.test1.contigs.fa.txt
-    ├── test-bacteria_odb10-busco -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco/
-    │   ├── logs/
-    │   │   └── busco.log
-    │   └── test1.contigs.fa/
-    │       ├── blast_db/
-    │       │   ├── test1.contigs.fa.ndb
-    │       │   ├── test1.contigs.fa.nhr
-    │       │   ├── test1.contigs.fa.nin
-    │       │   ├── test1.contigs.fa.not
-    │       │   ├── test1.contigs.fa.nsq
-    │       │   ├── test1.contigs.fa.ntf
-    │       │   └── test1.contigs.fa.nto
-    │       ├── logs/
-    │       │   ├── hmmsearch_err.log
-    │       │   ├── hmmsearch_out.log
-    │       │   ├── makeblastdb_err.log
-    │       │   ├── makeblastdb_out.log
-    │       │   ├── tblastn_err.log
-    │       │   └── tblastn_out.log
-    │       ├── run_bacteria_odb10/
-    │       │   ├── blast_output/
-    │       │   ├── busco_sequences/
-    │       │   ├── full_table.tsv
-    │       │   ├── hmmer_output/
-    │       │   ├── missing_busco_list.tsv
-    │       │   ├── short_summary.json
-    │       │   ├── short_summary.txt
-    │       │   └── single_copy_proteins.faa
-    │       └── translated_proteins/
-    │           ├── 1024388at2.faa
-    │           ├── 1054741at2.faa
-    │           ├── 1093223at2.faa
-    │           ├── 1151822at2.faa
-    │           ├── 143460at2.faa
-    │           ├── 1491686at2.faa
-    │           ├── 1504821at2.faa
-    │           ├── 1574817at2.faa
-    │           ├── 1592033at2.faa
-    │           ├── 1623045at2.faa
-    │           ├── 1661836at2.faa
-    │           ├── 1674344at2.faa
-    │           ├── 1698718at2.faa
-    │           ├── 1990650at2.faa
-    │           ├── 223233at2.faa
-    │           ├── 402899at2.faa
-    │           ├── 505485at2.faa
-    │           ├── 665824at2.faa
-    │           ├── 776861at2.faa
-    │           ├── 874197at2.faa
-    │           ├── 932854at2.faa
-    │           └── 95696at2.faa
-    ├── test-bacteria_odb10-busco.batch_summary.txt -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/test-bacteria_odb10-busco.batch_summary.txt
-    └── versions.yml -> /tmp/tmp6wqi0eyx/4f/ed0b23f0fc807bb68091298845c135/versions.yml
-    */
-
 }

tests/modules/busco/test.yml

@@ -16,19 +16,6 @@
         - "Complete BUSCOs"
         - "Missing BUSCOs"
         - "Dependencies and versions"
-    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "dataset"
-    - path: output/busco/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
-      contains:
-        - "BUSCO version"
-        - "The lineage dataset is"
-        - "BUSCO was run in mode"
-        - "Complete BUSCOs"
-        - "Missing BUSCOs"
-        - "Dependencies and versions"
     - path: output/busco/test-bacteria_odb10-busco.batch_summary.txt
       md5sum: bc2440f8a68d7fbf931ff911c1c3fdfa
     - path: output/busco/test-bacteria_odb10-busco/genome.fna/logs/bbtools_err.log
@@ -93,70 +80,6 @@
         - "DEBUG:busco.run_BUSCO"
         - "Results from dataset"
         - "how to cite BUSCO"
-    - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
-      md5sum: 5ad8ecfbf4058b059e5edeb9170fc683
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_err.log
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/bbtools_out.log
-      contains:
-        - "IUPAC"
-        - "genome scaffold"
-        - "Coverage"
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_err.log
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/hmmsearch_out.log
-      contains:
-        - "# hmmsearch :: search profile(s) against a sequence database"
-        - "# target sequence database:"
-        - "Internal pipeline statistics summary:"
-        - "[ok]"
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/logs/prodigal_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/.checkpoint
-      contains:
-        - "Tool: prodigal"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/predicted.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.faa
-      md5sum: 836e9a80d33d8b89168f07ddc13ee991
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11.fna
-      md5sum: 20eeb75f86842e6e136f02bca8b73a9f
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_err.log
-      md5sum: 538510cfc7483498210f01e53fe035ad
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/prodigal_output/predicted_genes/tmp/prodigal_mode_single_code_11_out.log
-      md5sum: 61050b0706addc9498b2088a2d6efa9a
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/.bbtools_output/.checkpoint
-      contains:
-        - "Tool: bbtools"
-        - "Completed"
-        - "jobs"
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/fragmented_busco_sequences.tar.gz
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/multi_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/busco_sequences/single_copy_busco_sequences.tar.gz
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/full_table.tsv
-      md5sum: 2360bb06f7171dafaa7ebf879789689b
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/hmmer_output.tar.gz
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/missing_busco_list.tsv
-      md5sum: e1fb12cf416448d35fbc5c508065963a
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.json
-      contains:
-        - "one_line_summary"
-        - "mode"
-        - "lineage_dataset"
-    - path: output/busco/test-bacteroidetes_odb10-busco/genome.fna/run_bacteroidetes_odb10/short_summary.txt
-      contains:
-        - "# BUSCO version is:"
-        - "Results:"
-        - "busco:"
-    - path: output/busco/test-bacteroidetes_odb10-busco/logs/busco.log
-      contains:
-        - "DEBUG:busco.run_BUSCO"
-        - "Results from dataset"
-        - "how to cite BUSCO"
 
 - name: busco test_busco_genome_multi_fasta
   command: nextflow run ./tests/modules/busco -entry test_busco_genome_multi_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/busco/nextflow.config

tests/modules/checkm/qa/main.nf

@@ -0,0 +1,44 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CHECKM_LINEAGEWF              } from '../../../../modules/checkm/lineagewf/main.nf'
+include { CHECKM_LINEAGEWF as CHECKM_LINEAGEWF_FASTA        } from '../../../../modules/checkm/lineagewf/main.nf'
+include { CHECKM_QA                     } from '../../../../modules/checkm/qa/main.nf'
+include { CHECKM_QA as CHECKM_QA_FASTA  } from '../../../../modules/checkm/qa/main.nf'
+
+workflow test_checkm_qa {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF ( input, fasta_ext, [] )
+
+    ch_checkmqa_input = CHECKM_LINEAGEWF.out.checkm_output
+        .join(CHECKM_LINEAGEWF.out.marker_file)
+        .map{
+            meta, dir, marker ->
+            [ meta, dir, marker, []]
+        }
+
+    CHECKM_QA ( ch_checkmqa_input, [] )
+}
+
+workflow test_checkm_qa_fasta {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
+    fasta_ext = 'fasta'
+
+    CHECKM_LINEAGEWF_FASTA ( input, fasta_ext, [] )
+
+    ch_checkmqa_input =  CHECKM_LINEAGEWF_FASTA.out.checkm_output
+        .join(CHECKM_LINEAGEWF_FASTA.out.marker_file)
+        .map{
+            meta, dir, marker ->
+            [ meta, dir, marker, []]
+        }
+
+    CHECKM_QA_FASTA ( ch_checkmqa_input, [] )
+}

tests/modules/checkm/qa/nextflow.config

@@ -0,0 +1,16 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: CHECKM_QA {
+        ext.prefix = { "${meta.id}.qa" }
+    }
+
+
+    withName: CHECKM_QA_FASTA {
+        ext.args = "-o 9"
+        ext.prefix = { "${meta.id}.qa" }
+    }
+
+
+}

tests/modules/checkm/qa/test.yml

@@ -0,0 +1,16 @@
+- name: checkm qa test_checkm_qa
+  command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa -c ./tests/config/nextflow.config  -c ./tests/modules/checkm/qa/nextflow.config
+  tags:
+    - checkm/qa
+    - checkm
+  files:
+    - path: output/checkm/test.qa.txt
+      md5sum: 645f4282569afb4b171396732b2d2582
+
+- name: checkm qa test_checkm_qa_fasta
+  command: nextflow run ./tests/modules/checkm/qa -entry test_checkm_qa_fasta -c ./tests/config/nextflow.config  -c ./tests/modules/checkm/qa/nextflow.config
+  tags:
+    - checkm/qa
+    - checkm
+  files:
+    - path: output/checkm/test.qa.fasta

tests/modules/fcs/fcsadaptor/main.nf

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

tests/modules/fcs/fcsadaptor/nextflow.config

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

tests/modules/fcs/fcsadaptor/test.yml

@@ -0,0 +1,15 @@
+- name: fcs fcsadaptor test_fcs_fcsadaptor
+  command: nextflow run ./tests/modules/fcs/fcsadaptor -entry test_fcs_fcsadaptor -c ./tests/config/nextflow.config  -c ./tests/modules/fcs/fcsadaptor/nextflow.config
+  tags:
+    - fcs/fcsadaptor
+    - fcs
+  files:
+    - path: output/fcs/test.cleaned_sequences.fa.gz
+      md5sum: 2f331e59b352418420a35236091bf93c
+    - path: output/fcs/test.fcs_adaptor.log
+      contains: ["Original command:", "Executing:", "INFO:cwltool:[workflow ] completed success"]
+    - path: output/fcs/test.fcs_adaptor_report.txt
+      md5sum: 27375be4671e01d2d2674ddd1d44414a
+    - path: output/fcs/test.pipeline_args.yaml
+      md5sum: 80effed2a75550a6a861c47f4c30449d
+    - path: output/fcs/test.skipped_trims.jsonl

tests/modules/hisat2/align/test.yml

@@ -7,7 +7,6 @@
     - path: output/hisat2/test.hisat2.summary.log
       md5sum: 7b8a9e61b7646da1089b041333c41a87
     - path: output/hisat2/genome.splice_sites.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/hisat2/test.bam
     - path: output/hisat2/hisat2/genome.5.ht2
       md5sum: 91198831aaba993acac1734138c5f173
@@ -35,7 +34,6 @@
     - path: output/hisat2/test.hisat2.summary.log
       md5sum: 9839b31db795958cc4b70711a3414e9c
     - path: output/hisat2/genome.splice_sites.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/hisat2/test.bam
     - path: output/hisat2/hisat2/genome.5.ht2
       md5sum: 91198831aaba993acac1734138c5f173

tests/modules/hisat2/build_test/test.yml

@@ -5,7 +5,6 @@
     - hisat2/build
   files:
     - path: output/hisat2/genome.splice_sites.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/hisat2/hisat2/genome.5.ht2
       md5sum: 91198831aaba993acac1734138c5f173
     - path: output/hisat2/hisat2/genome.7.ht2

tests/modules/hisat2/extractsplicesites/test.yml

@@ -5,4 +5,3 @@
     - hisat2/extractsplicesites
   files:
     - path: output/hisat2/genome.splice_sites.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e

tests/modules/vcflib/vcfbreakmulti/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { VCFLIB_VCFBREAKMULTI } from '../../../../modules/vcflib/vcfbreakmulti/main.nf'
+
+workflow test_vcflib_vcfbreakmulti {
+
+    input = [
+        [ id:'test', 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)
+    ]
+
+    VCFLIB_VCFBREAKMULTI ( input )
+}

tests/modules/vcflib/vcfbreakmulti/nextflow.config

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

tests/modules/vcflib/vcfbreakmulti/test.yml

@@ -0,0 +1,16 @@
+- name: vcflib vcfbreakmulti
+  command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config
+  tags:
+    - vcflib/vcfbreakmulti
+    - vcflib
+  files:
+    - path: output/vcflib/test.breakmulti.vcf.gz
+      md5sum: 666d2d970399cf219dc1dc1eadff9170
+
+- name: vcflib vcfbreakmulti stub
+  command: nextflow run ./tests/modules/vcflib/vcfbreakmulti -entry test_vcflib_vcfbreakmulti -c tests/config/nextflow.config -stub
+  tags:
+    - vcflib/vcfbreakmulti
+    - vcflib
+  files:
+    - path: output/vcflib/test.breakmulti.vcf.gz