Merge branch 'master' into motus_profile

modules/busco/main.nf

@@ -0,0 +1,84 @@
+process BUSCO {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::busco=5.3.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/busco:5.3.2--pyhdfd78af_0':
+        'quay.io/biocontainers/busco:5.3.2--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path('tmp_input/*')
+    each 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
+
+    output:
+    tuple val(meta), path("*-busco.batch_summary.txt"), emit: batch_summary
+    tuple val(meta), path("short_summary.*.txt")      , emit: short_summaries_txt, optional: true
+    tuple val(meta), path("short_summary.*.json")     , emit: short_summaries_json, optional: true
+    tuple val(meta), path("*-busco")                  , emit: busco_dir
+    path "versions.yml"                               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
+    def busco_config = config_file ? "--config $config_file" : ''
+    def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
+    def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
+    """
+    # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
+    # Check for container variable initialisation script and source it.
+    if [ -f "/usr/local/env-activate.sh" ]; then
+        set +u  # Otherwise, errors out because of various unbound variables
+        . "/usr/local/env-activate.sh"
+        set -u
+    fi
+
+    # If the augustus config directory is not writable, then copy to writeable area
+    if [ ! -w "\${AUGUSTUS_CONFIG_PATH}" ]; then
+        # Create writable tmp directory for augustus
+        AUG_CONF_DIR=\$( mktemp -d -p \$PWD )
+        cp -r \$AUGUSTUS_CONFIG_PATH/* \$AUG_CONF_DIR
+        export AUGUSTUS_CONFIG_PATH=\$AUG_CONF_DIR
+        echo "New AUGUSTUS_CONFIG_PATH=\${AUGUSTUS_CONFIG_PATH}"
+    fi
+
+    # Ensure the input is uncompressed
+    INPUT_SEQS=input_seqs
+    mkdir "\$INPUT_SEQS"
+    cd "\$INPUT_SEQS"
+    for FASTA in ../tmp_input/*; do
+        if [ "\${FASTA##*.}" == 'gz' ]; then
+            gzip -cdf "\$FASTA" > \$( basename "\$FASTA" .gz )
+        else
+            ln -s "\$FASTA" .
+        fi
+    done
+    cd ..
+
+    busco \\
+        --cpu $task.cpus \\
+        --in "\$INPUT_SEQS" \\
+        --out ${prefix}-busco \\
+        $busco_lineage \\
+        $busco_lineage_dir \\
+        $busco_config \\
+        $args
+
+    # clean up
+    rm -rf "\$INPUT_SEQS"
+
+    # Move files to avoid staging/publishing issues
+    mv ${prefix}-busco/batch_summary.txt ${prefix}-busco.batch_summary.txt
+    mv ${prefix}-busco/*/short_summary.*.{json,txt} . || echo "Short summaries were not available: No genes were found."
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        busco: \$( busco --version 2>&1 | sed 's/^BUSCO //' )
+    END_VERSIONS
+    """
+}

modules/busco/meta.yml

@@ -0,0 +1,69 @@
+name: busco
+description: Benchmarking Universal Single Copy Orthologs
+keywords:
+  - quality control
+  - genome
+  - transcriptome
+  - proteome
+tools:
+  - busco:
+      description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
+      homepage: https://busco.ezlab.org/
+      documentation: https://busco.ezlab.org/busco_userguide.html
+      tool_dev_url: https://gitlab.com/ezlab/busco
+      doi: "10.1007/978-1-4939-9173-0_14"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Nucleic or amino acid sequence file in FASTA format.
+      pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+  - lineage:
+      type: value
+      description: The BUSCO lineage to use, or "auto" to automatically select lineage
+  - busco_lineages_path:
+      type: directory
+      description: Path to local BUSCO lineages directory.
+  - config_file:
+      type: file
+      description: Path to BUSCO config file.
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - batch_summary:
+      type: file
+      description: Summary of all sequence files analyzed
+      pattern: "*-busco.batch_summary.txt"
+  - short_summaries_txt:
+      type: file
+      description: Short Busco summary in plain text format
+      pattern: "short_summary.*.txt"
+  - short_summaries_json:
+      type: file
+      description: Short Busco summary in JSON format
+      pattern: "short_summary.*.json"
+  - busco_dir:
+      type: directory
+      description: BUSCO lineage specific output
+      pattern: "*-busco"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@priyanka-surana"
+  - "@charles-plessy"
+  - "@mahesh-panchal"
+  - "@muffato"
+  - "@jvhagey"

modules/snapaligner/align/main.nf

@@ -1,4 +1,4 @@
-process SNAPALIGNER_PAIRED {
+process SNAPALIGNER_ALIGN {
     tag '$meta.id'
     label 'process_high'
 
@@ -21,15 +21,16 @@ process SNAPALIGNER_PAIRED {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def subcmd = meta.single_end ? "single" : "paired"
 
     """
     mkdir -p index
     mv $index index/
 
-    snap-aligner paired \\
+    snap-aligner ${subcmd} \\
         index \\
         ${reads.join(" ")} \\
-        -o -bam ${prefix}.bam \\
+        -o ${prefix}.bam \\
         -t ${task.cpus} \\
         $args
 

modules/snapaligner/align/meta.yml

@@ -1,5 +1,5 @@
-name: "snapaligner_paired"
+name: "snapaligner_align"
-description: Performs paired end fastq alignment to a fasta reference using SNAP
+description: Performs fastq alignment to a fasta reference using SNAP
 keywords:
   - alignment
   - map
@@ -22,7 +22,7 @@ input:
         e.g. [ id:'test', single_end:false ]
   - reads:
       type: file
-      description: List of input fastq files of size 2 for fastq or 1 for bam
+      description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
       pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
   - index:
       type: file

modules/snapaligner/single/main.nf

@@ -1,41 +0,0 @@
-process SNAPALIGNER_SINGLE {
-    tag '$meta.id'
-    label 'process_high'
-
-    conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
-        'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
-
-    input:
-    tuple val(meta), path(reads)
-    path index
-
-    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}"
-
-    """
-    mkdir -p index
-    mv $index index/
-
-    snap-aligner single \\
-        index \\
-        ${reads.join(" ")} \\
-        -o -bam ${prefix}.bam \\
-        -t ${task.cpus} \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/.\$//')
-    END_VERSIONS
-    """
-}

modules/snapaligner/single/meta.yml

@@ -1,48 +0,0 @@
-name: "snapaligner_single"
-description: Performs single end fastq alignment to a fasta reference using SNAP
-keywords:
-  - alignment
-  - map
-  - fastq
-  - bam
-  - sam
-tools:
-  - "snapaligner":
-      description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
-      homepage: "http://snap.cs.berkeley.edu"
-      documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
-      tool_dev_url: "https://github.com/amplab/snap"
-      doi: "10.1101/2021.11.23.469039"
-      licence: "['Apache v2']"
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: List of single end input files
-      pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
-  - index:
-      type: file
-      description: List of SNAP genome index files
-      pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
-
-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: Aligned BAM file
-      pattern: "*.{bam}"
-
-authors:
-  - "@matthdsm"

modules/sratools/prefetch/main.nf

@@ -1,43 +1,26 @@
 process SRATOOLS_PREFETCH {
     tag "$id"
     label 'process_low'
-    label 'error_retry'
 
     conda (params.enable_conda ? 'bioconda::sra-tools=2.11.0' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5262h314213e_0' :
+        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'quay.io/biocontainers/sra-tools:2.11.0--pl5262h314213e_0' }"
+        'quay.io/biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
 
     input:
     tuple val(meta), val(id)
 
     output:
-    tuple val(meta), path("$id"), emit: sra
+    tuple val(meta), path(id), emit: sra
     path "versions.yml"         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
-    script:
+    shell:
-    def args = task.ext.args ?: ''
+    args = task.ext.args ?: ''
-    def config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
+    args2 = task.ext.args2 ?: '5 1 100'  // <num retries> <base delay in seconds> <max delay in seconds>
-    """
+    config = "/LIBS/GUID = \"${UUID.randomUUID().toString()}\"\\n/libs/cloud/report_instance_identity = \"true\"\\n"
-    eval "\$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
-    if [[ ! -f "\${NCBI_SETTINGS}" ]]; then
-        mkdir -p "\$(dirname "\${NCBI_SETTINGS}")"
-        printf '${config}' > "\${NCBI_SETTINGS}"
-    fi
 
-    prefetch \\
+    template 'retry_with_backoff.sh'
-        $args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
 }

modules/sratools/prefetch/templates/retry_with_backoff.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+
+set -u
+
+retry_with_backoff() {
+    local max_attempts=${1}
+    local delay=${2}
+    local max_time=${3}
+    local attempt=1
+    local output=
+    local status=
+
+    # Remove the first three arguments to this function in order to access
+    # the 'real' command with `${@}`.
+    shift 3
+
+    while [ ${attempt} -le ${max_attempts} ]; do
+        output=$("${@}")
+        status=${?}
+
+        if [ ${status} -eq 0 ]; then
+            break
+        fi
+
+        if [ ${attempt} -lt ${max_attempts} ]; then
+            echo "Failed attempt ${attempt} of ${max_attempts}. Retrying in ${delay} s." >&2
+            sleep ${delay}
+        elif [ ${attempt} -eq ${max_attempts} ]; then
+            echo "Failed after ${attempt} attempts." >&2
+            return ${status}
+        fi
+
+        attempt=$(( ${attempt} + 1 ))
+        delay=$(( ${delay} * 2 ))
+        if [ ${delay} -ge ${max_time} ]; then
+            delay=${max_time}
+        fi
+    done
+
+    echo "${output}"
+}
+
+eval "$(vdb-config -o n NCBI_SETTINGS | sed 's/[" ]//g')"
+if [[ ! -f "${NCBI_SETTINGS}" ]]; then
+    mkdir -p "$(dirname "${NCBI_SETTINGS}")"
+    printf '!{config}' > "${NCBI_SETTINGS}"
+fi
+
+retry_with_backoff !{args2} \
+    prefetch \
+    !{args} \
+    !{id}
+
+vdb-validate !{id}
+
+cat <<-END_VERSIONS > versions.yml
+"!{task.process}":
+    sratools: $(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+END_VERSIONS

tests/config/pytest_modules.yml

@@ -337,6 +337,10 @@ bracken/bracken:
   - modules/bracken/bracken/**
   - tests/modules/bracken/bracken/**
 
+busco:
+  - modules/busco/**
+  - tests/modules/busco/**
+
 bwa/aln:
   - modules/bwa/aln/**
   - tests/modules/bwa/aln/**
@@ -1767,13 +1771,9 @@ snapaligner/index:
   - modules/snapaligner/index/**
   - tests/modules/snapaligner/index/**
 
-snapaligner/paired:
+snapaligner/align:
-  - modules/snapaligner/paired/**
+  - modules/snapaligner/align/**
-  - tests/modules/snapaligner/paired/**
+  - tests/modules/snapaligner/align/**
-
-snapaligner/single:
-  - modules/snapaligner/single/**
-  - tests/modules/snapaligner/single/**
 
 snpdists:
   - modules/snpdists/**

tests/config/test_data.config

@@ -125,6 +125,7 @@ params {
                 genome_gff3                                    = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gff3"
                 genome_gtf                                     = "${test_data_dir}/genomics/homo_sapiens/genome/genome.gtf"
                 genome_interval_list                           = "${test_data_dir}/genomics/homo_sapiens/genome/genome.interval_list"
+                genome_multi_interval_bed                      = "${test_data_dir}/genomics/homo_sapiens/genome/genome.multi_intervals.bed"
                 genome_sizes                                   = "${test_data_dir}/genomics/homo_sapiens/genome/genome.sizes"
                 genome_bed                                     = "${test_data_dir}/genomics/homo_sapiens/genome/genome.bed"
                 genome_header                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
@@ -211,6 +212,7 @@ params {
                 test_paired_end_hla                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.bam"
                 test_paired_end_hla_sorted_bam                          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam"
                 test_paired_end_hla_sorted_bam_bai                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/example_hla_pe.sorted.bam.bai"
+
                 test2_paired_end_sorted_bam                             = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam"
                 test2_paired_end_sorted_bam_bai                         = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai"
                 test2_paired_end_name_sorted_bam                        = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
@@ -225,7 +227,6 @@ params {
                 test2_paired_end_umi_unsorted_bam                       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
                 test2_paired_end_umi_unsorted_tagged_bam                = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
 
-
                 mitochon_standin_recalibrated_sorted_bam                = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
                 mitochon_standin_recalibrated_sorted_bam_bai            = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
 

tests/modules/busco/main.nf

@@ -0,0 +1,404 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BUSCO } from '../../../modules/busco/main.nf'
+
+workflow test_busco_genome_single_fasta {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        ['bacteria_odb10', 'bacteroidetes_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
+
+    Former Output tree -w 'auto':
+    /tmp/tmp846crjv2/busco/
+    ├── short_summary.generic.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.json
+    ├── short_summary.generic.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.generic.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteria_odb10.genome.fna.json -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.json
+    ├── short_summary.specific.bacteria_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/short_summary.specific.bacteria_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.json -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidales_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/short_summary.specific.bacteroidales_odb10.genome.fna.txt
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.json -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+    ├── short_summary.specific.bacteroidetes_odb10.genome.fna.txt -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/short_summary.specific.bacteroidetes_odb10.genome.fna.txt
+    ├── test-auto-busco -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/
+    │   ├── genome.fna/
+    │   │   ├── auto_lineage/
+    │   │   │   ├── run_archaea_odb10/
+    │   │   │   ├── run_bacteria_odb10/
+    │   │   │   └── run_eukaryota_odb10/
+    │   │   ├── logs/
+    │   │   │   ├── hmmsearch_err.log
+    │   │   │   ├── hmmsearch_out.log
+    │   │   │   ├── metaeuk_err.log
+    │   │   │   ├── metaeuk_out.log
+    │   │   │   ├── prodigal_err.log
+    │   │   │   ├── prodigal_out.log
+    │   │   │   ├── sepp_err.log
+    │   │   │   └── sepp_out.log
+    │   │   ├── prodigal_output/
+    │   │   │   └── predicted_genes/
+    │   │   ├── run_bacteria_odb10 -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco/genome.fna/auto_lineage/run_bacteria_odb10/  [recursive, not followed]
+    │   │   └── run_bacteroidales_odb10/
+    │   │       ├── busco_sequences/
+    │   │       ├── full_table.tsv
+    │   │       ├── hmmer_output/
+    │   │       ├── missing_busco_list.tsv
+    │   │       ├── short_summary.json
+    │   │       └── short_summary.txt
+    │   └── logs/
+    │       └── busco.log
+    ├── test-auto-busco.batch_summary.txt -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/test-auto-busco.batch_summary.txt
+    ├── test-bacteria_odb10-busco -> /tmp/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/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/tmpi6af66j1/45/107812e983a8e695c380ebc215e7d9/test-bacteria_odb10-busco.batch_summary.txt
+    ├── test-bacteroidetes_odb10-busco -> /tmp/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/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/tmpi6af66j1/a2/eb4a34894f3ac5554759ad6c9f652b/test-bacteroidetes_odb10-busco.batch_summary.txt
+    └── versions.yml -> /tmp/tmpi6af66j1/18/8be22ecd7a71471ff5082bd512972b/versions.yml
+    */
+
+}
+
+workflow test_busco_genome_multi_fasta {
+
+    input = [
+        [ id:'test' ], // meta map
+        [
+            file( params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true),
+            file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['genome_fasta'], checkIfExists: true)
+        ]
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // 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 {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [], // 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 {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'eukaryota_odb10',
+        [], // Download busco lineage
+        [], // 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 {
+
+    input = [
+        [ id:'test' ], // meta map
+        file( params.test_data['candidatus_portiera_aleyrodidarum']['genome']['proteome_fasta'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // 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 = [
+        [ id:'test' ], // meta map
+        file( params.test_data['bacteroides_fragilis']['illumina']['test1_contigs_fa_gz'], checkIfExists: true)
+    ]
+
+    BUSCO (
+        input,
+        'bacteria_odb10',
+        [], // Download busco lineage
+        [], // 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/nextflow.config

@@ -0,0 +1,28 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'test_busco_genome_single_fasta:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_genome_multi_fasta:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_eukaryote_metaeuk:BUSCO' {
+        ext.args = '--mode genome'
+    }
+
+    withName: 'test_busco_eukaryote_augustus:BUSCO' {
+        ext.args = '--mode genome --augustus'
+    }
+
+    withName: 'test_busco_protein:BUSCO' {
+        ext.args = '--mode proteins'
+    }
+
+    withName: 'test_busco_transcriptome:BUSCO'{
+        ext.args = '--mode transcriptome'
+    }
+}

tests/modules/busco/test.yml

@@ -0,0 +1,159 @@
+- name: busco test_busco_genome_single_fasta
+  command: nextflow run tests/modules/busco -entry test_busco_genome_single_fasta -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_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/short_summary.specific.bacteroidetes_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "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: e50690742e9ae6abdd2bf99334ff9e12
+    - path: output/busco/test-bacteroidetes_odb10-busco.batch_summary.txt
+      md5sum: 4c1b2c4317c88398eddc30877ed740d9
+    - path: output/busco/versions.yml
+      md5sum: 8aa830f71587d859df35c6cfab59f35d
+
+- name: busco test_busco_genome_multi_fasta
+  command: nextflow run tests/modules/busco -entry test_busco_genome_multi_fasta -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fasta.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/short_summary.specific.bacteria_odb10.genome.fna.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_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: 5360dfe83bec1f5741ee115e53e6b517
+    - path: output/busco/versions.yml
+      md5sum: 9a959eb0a1f765777dff1ea2f5c139c0
+
+- name: busco test_busco_eukaryote_metaeuk
+  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_metaeuk -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.eukaryota_odb10.genome.fasta.txt
+      contains:
+        - "BUSCO version"
+        - "The lineage dataset is"
+        - "BUSCO was run in mode"
+        - "Complete BUSCOs"
+        - "Missing BUSCOs"
+        - "Dependencies and versions"
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: a70806f99ba5706d7353d3353b3f1d2b
+    - path: output/busco/versions.yml
+      md5sum: 34a808c257e6db1b0456f3b4372bc477
+
+- name: busco test_busco_eukaryote_augustus
+  command: nextflow run tests/modules/busco -entry test_busco_eukaryote_augustus -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/test-eukaryota_odb10-busco.batch_summary.txt
+      md5sum: 660393dd43cd6a093b952d4b8ad41e40
+    - path: output/busco/versions.yml
+      md5sum: 2caac915461410b16a1524ac064cd0df
+
+- name: busco test_busco_protein
+  command: nextflow run tests/modules/busco -entry test_busco_protein -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.proteome.fasta.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: fd3b4e30ce74d1fcb95d6286d6e2049f
+    - path: output/busco/versions.yml
+      md5sum: d7392261a57960a7e6aea609dce824f5
+
+- name: busco test_busco_transcriptome
+  command: nextflow run tests/modules/busco -entry test_busco_transcriptome -c tests/config/nextflow.config
+  tags:
+    - busco
+  files:
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.json
+      contains:
+        - "one_line_summary"
+        - "input_file"
+        - "mode"
+        - "dataset"
+    - path: output/busco/short_summary.specific.bacteria_odb10.test1.contigs.fa.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: 9a176cafe66ac0adca89dc34ad2be13f
+    - path: output/busco/versions.yml
+      md5sum: 30eacbc7df70f6b1e72e0a7b6d02a7e1

tests/modules/snapaligner/align/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SNAPALIGNER_INDEX                       } from '../../../../modules/snapaligner/index/main.nf'
+include { SNAPALIGNER_ALIGN as SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/align/main.nf'
+include { SNAPALIGNER_ALIGN as SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/align/main.nf'
+
+workflow test_snapaligner_single {
+
+    input = [
+        [ id:'test', single_end:true ], // meta map
+        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
+    ]
+
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+    SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
+}
+
+workflow test_snapaligner_paired {
+
+    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)]
+    ]
+
+    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
+    SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
+}

tests/modules/snapaligner/align/test.yml

@@ -0,0 +1,19 @@
+- name: snapaligner align test_snapaligner_single
+  command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_single -c tests/config/nextflow.config
+  tags:
+    - snapaligner/align
+    - snapaligner
+  files:
+    - path: output/snapaligner/test.bam
+      md5sum: 5d95594e4ef1ee23ce56e6a7cb64f0f2
+    - path: output/snapaligner/versions.yml
+
+- name: snapaligner align test_snapaligner_paired
+  command: nextflow run tests/modules/snapaligner/align -entry test_snapaligner_paired -c tests/config/nextflow.config
+  tags:
+    - snapaligner/align
+    - snapaligner
+  files:
+    - path: output/snapaligner/test.bam
+      md5sum: a1405da5876f15dbe8a81516b94c2a15
+    - path: output/snapaligner/versions.yml

tests/modules/snapaligner/paired/main.nf

@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
-include { SNAPALIGNER_PAIRED } from '../../../../modules/snapaligner/paired/main.nf'
-
-workflow test_snapaligner_paired {
-
-    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)]
-    ]
-
-    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_PAIRED ( input, SNAPALIGNER_INDEX.out.index )
-}

tests/modules/snapaligner/paired/test.yml

@@ -1,9 +0,0 @@
-- name: snapaligner paired test_snapaligner_paired
-  command: nextflow run tests/modules/snapaligner/paired -entry test_snapaligner_paired -c tests/config/nextflow.config
-  tags:
-    - snapaligner
-    - snapaligner/paired
-  files:
-    - path: output/snapaligner/test.bam
-      md5sum: 2ac92e9539fa246dd6db52b5de56fca5
-    - path: output/snapaligner/versions.yml

tests/modules/snapaligner/single/main.nf

@@ -1,17 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
-include { SNAPALIGNER_SINGLE } from '../../../../modules/snapaligner/single/main.nf'
-
-workflow test_snapaligner_single {
-
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        [file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
-    ]
-
-    SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
-    SNAPALIGNER_SINGLE ( input, SNAPALIGNER_INDEX.out.index )
-}

tests/modules/snapaligner/single/nextflow.config

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

tests/modules/snapaligner/single/test.yml

@@ -1,9 +0,0 @@
-- name: snapaligner single test_snapaligner_single
-  command: nextflow run tests/modules/snapaligner/single -entry test_snapaligner_single -c tests/config/nextflow.config
-  tags:
-    - snapaligner/single
-    - snapaligner
-  files:
-    - path: output/snapaligner/test.bam
-      md5sum: 696f7ea8e1aa5f9d7dafb9d0134fe25d
-    - path: output/snapaligner/versions.yml

tests/subworkflows/nf-core/annotation/snpeff/main.nf

@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main'
+include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation/snpeff/main'
 
 workflow annotation_snpeff {
     input = [