diff --git a/modules/snapaligner/paired/main.nf b/modules/snapaligner/align/main.nf
similarity index 87%
rename from modules/snapaligner/paired/main.nf
rename to modules/snapaligner/align/main.nf
index 57044893..ef7af561 100644
--- a/modules/snapaligner/paired/main.nf
+++ b/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
 
diff --git a/modules/snapaligner/paired/meta.yml b/modules/snapaligner/align/meta.yml
similarity index 86%
rename from modules/snapaligner/paired/meta.yml
rename to modules/snapaligner/align/meta.yml
index b19e0174..611b0b71 100644
--- a/modules/snapaligner/paired/meta.yml
+++ b/modules/snapaligner/align/meta.yml
@@ -1,5 +1,5 @@
-name: "snapaligner_paired"
-description: Performs paired end fastq alignment to a fasta reference using SNAP
+name: "snapaligner_align"
+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
diff --git a/modules/snapaligner/single/main.nf b/modules/snapaligner/single/main.nf
deleted file mode 100644
index b13e1153..00000000
--- a/modules/snapaligner/single/main.nf
+++ /dev/null
@@ -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
-    """
-}
diff --git a/modules/snapaligner/single/meta.yml b/modules/snapaligner/single/meta.yml
deleted file mode 100644
index e69cc721..00000000
--- a/modules/snapaligner/single/meta.yml
+++ /dev/null
@@ -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"
diff --git a/modules/sratools/prefetch/main.nf b/modules/sratools/prefetch/main.nf
index 2233d0aa..3408c3e9 100644
--- a/modules/sratools/prefetch/main.nf
+++ b/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' :
-        'quay.io/biocontainers/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--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:
-    def args = task.ext.args ?: ''
-    def 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
+    shell:
+    args = task.ext.args ?: ''
+    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"
 
-    prefetch \\
-        $args \\
-        --progress \\
-        $id
-
-    vdb-validate $id
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
-    END_VERSIONS
-    """
+    template 'retry_with_backoff.sh'
 }
diff --git a/modules/sratools/prefetch/templates/retry_with_backoff.sh b/modules/sratools/prefetch/templates/retry_with_backoff.sh
new file mode 100755
index 00000000..fbcb6532
--- /dev/null
+++ b/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
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index d01d08e8..04b13de7 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1771,13 +1771,9 @@ snapaligner/index:
   - modules/snapaligner/index/**
   - tests/modules/snapaligner/index/**
 
-snapaligner/paired:
-  - modules/snapaligner/paired/**
-  - tests/modules/snapaligner/paired/**
-
-snapaligner/single:
-  - modules/snapaligner/single/**
-  - tests/modules/snapaligner/single/**
+snapaligner/align:
+  - modules/snapaligner/align/**
+  - tests/modules/snapaligner/align/**
 
 snpdists:
   - modules/snpdists/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index e9a5f4ab..4ff6efd9 100644
--- a/tests/config/test_data.config
+++ b/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                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome.header"
@@ -181,16 +182,16 @@ params {
                 vcfanno_toml                                   = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/vcfanno/vcfanno.toml"
             }
             'pangenome' {
-                pangenome_fa                                  = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
-                pangenome_fa_gz                               = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
-                pangenome_paf                                 = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
-                pangenome_paf_gz                              = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
-                pangenome_seqwish_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
-                pangenome_smoothxg_gfa                        = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
-                pangenome_gfaffix_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
+                pangenome_fa                                   = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa"
+                pangenome_fa_gz                                = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.fa.gz"
+                pangenome_paf                                  = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf"
+                pangenome_paf_gz                               = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.paf.gz"
+                pangenome_seqwish_gfa                          = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.seqwish.gfa"
+                pangenome_smoothxg_gfa                         = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.smoothxg.gfa"
+                pangenome_gfaffix_gfa                          = "${test_data_dir}/pangenomics/homo_sapiens/pangenome.gfaffix.gfa"
                 'odgi' {
-                    pangenome_og                                  = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
-                    pangenome_lay                                 = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
+                    pangenome_og                               = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.og"
+                    pangenome_lay                              = "${test_data_dir}/pangenomics/homo_sapiens/odgi/pangenome.lay"
                 }
             }
             'illumina' {
@@ -211,131 +212,131 @@ 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"
-                test2_paired_end_markduplicates_sorted_bam     = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
-                test2_paired_end_markduplicates_sorted_bam_bai = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
-                test2_paired_end_recalibrated_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
-                test2_paired_end_recalibrated_sorted_bam_bai   = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
-                test2_paired_end_umi_consensus_bam             = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
-                test2_paired_end_umi_converted_bam             = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
-                test2_paired_end_umi_grouped_bam               = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
-                test2_paired_end_umi_histogram_txt             = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
-                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"
 
+                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                        = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.name.sorted.bam"
+                test2_paired_end_markduplicates_sorted_bam              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam"
+                test2_paired_end_markduplicates_sorted_bam_bai          = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.markduplicates.sorted.bam.bai"
+                test2_paired_end_recalibrated_sorted_bam                = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam"
+                test2_paired_end_recalibrated_sorted_bam_bai            = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test2.paired_end.recalibrated.sorted.bam.bai"
+                test2_paired_end_umi_consensus_bam                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_consensus.bam"
+                test2_paired_end_umi_converted_bam                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_converted.bam"
+                test2_paired_end_umi_grouped_bam                        = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_grouped.bam"
+                test2_paired_end_umi_histogram_txt                      = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_histogram.txt"
+                test2_paired_end_umi_unsorted_bam                       = "${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"
+                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"
 
-                test_paired_end_sorted_cram                      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
-                test_paired_end_sorted_cram_crai                 = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
-                test_paired_end_markduplicates_sorted_cram       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
-                test_paired_end_markduplicates_sorted_cram_crai  = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
-                test_paired_end_recalibrated_sorted_cram         = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
-                test_paired_end_recalibrated_sorted_cram_crai    = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
+                test_paired_end_sorted_cram                             = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
+                test_paired_end_sorted_cram_crai                        = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
+                test_paired_end_markduplicates_sorted_cram              = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
+                test_paired_end_markduplicates_sorted_cram_crai         = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
+                test_paired_end_recalibrated_sorted_cram                = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
+                test_paired_end_recalibrated_sorted_cram_crai           = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
 
-                test2_paired_end_sorted_cram                     = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
-                test2_paired_end_sorted_cram_crai                = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
-                test2_paired_end_markduplicates_sorted_cram      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
-                test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
-                test2_paired_end_recalibrated_sorted_cram        = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
-                test2_paired_end_recalibrated_sorted_cram_crai   = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
+                test2_paired_end_sorted_cram                            = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
+                test2_paired_end_sorted_cram_crai                       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
+                test2_paired_end_markduplicates_sorted_cram             = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
+                test2_paired_end_markduplicates_sorted_cram_crai        = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
+                test2_paired_end_recalibrated_sorted_cram               = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
+                test2_paired_end_recalibrated_sorted_cram_crai          = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
 
-                test_1_fastq_gz                                = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
-                test_2_fastq_gz                                = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
-                test_umi_1_fastq_gz                            = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
-                test_umi_2_fastq_gz                            = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
-                test2_1_fastq_gz                               = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
-                test2_2_fastq_gz                               = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
-                test2_umi_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
-                test2_umi_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
-                test_rnaseq_1_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
-                test_rnaseq_2_fastq_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
+                test_1_fastq_gz                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
+                test_2_fastq_gz                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
+                test_umi_1_fastq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"
+                test_umi_2_fastq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_2.fastq.gz"
+                test2_1_fastq_gz                                        = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_1.fastq.gz"
+                test2_2_fastq_gz                                        = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2_2.fastq.gz"
+                test2_umi_1_fastq_gz                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_1.fastq.gz"
+                test2_umi_2_fastq_gz                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test2.umi_2.fastq.gz"
+                test_rnaseq_1_fastq_gz                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz"
+                test_rnaseq_2_fastq_gz                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz"
 
-                test_baserecalibrator_table                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
-                test2_baserecalibrator_table                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
-                test_pileups_table                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
-                test2_pileups_table                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
+                test_baserecalibrator_table                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table"
+                test2_baserecalibrator_table                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.baserecalibrator.table"
+                test_pileups_table                                      = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
+                test2_pileups_table                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
 
-                test_genomicsdb_tar_gz                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
-                test_pon_genomicsdb_tar_gz                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
+                test_genomicsdb_tar_gz                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
+                test_pon_genomicsdb_tar_gz                              = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
 
-                test2_haplotc_ann_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
-                test2_haplotc_ann_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
+                test2_haplotc_ann_vcf_gz                                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
+                test2_haplotc_ann_vcf_gz_tbi                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
 
-                test2_recal                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
-                test2_recal_idx                                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
-                test2_tranches                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
-                test2_allele_specific_recal                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
-                test2_allele_specific_recal_idx                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
-                test2_allele_specific_tranches                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
+                test2_recal                                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
+                test2_recal_idx                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
+                test2_tranches                                          = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"
+                test2_allele_specific_recal                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal"
+                test2_allele_specific_recal_idx                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.recal.idx"
+                test2_allele_specific_tranches                          = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2_allele_specific.tranches"
 
-                test_test2_paired_mutect2_calls_vcf_gz         = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
-                test_test2_paired_mutect2_calls_vcf_gz_tbi     = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
-                test_test2_paired_mutect2_calls_vcf_gz_stats   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
-                test_test2_paired_mutect2_calls_f1r2_tar_gz    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
-                test_test2_paired_mutect2_calls_artifact_prior_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
-                test_test2_paired_segmentation_table           = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
-                test_test2_paired_contamination_table          = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
+                test_test2_paired_mutect2_calls_vcf_gz                  = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz"
+                test_test2_paired_mutect2_calls_vcf_gz_tbi              = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.tbi"
+                test_test2_paired_mutect2_calls_vcf_gz_stats            = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.vcf.gz.stats"
+                test_test2_paired_mutect2_calls_f1r2_tar_gz             = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/paired_mutect2_calls/test_test2_paired_mutect2_calls.f1r2.tar.gz"
+                test_test2_paired_mutect2_calls_artifact_prior_tar_gz   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired_mutect2_calls.artifact-prior.tar.gz"
+                test_test2_paired_segmentation_table                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.segmentation.table"
+                test_test2_paired_contamination_table                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_test2_paired.contamination.table"
 
-                test_genome_vcf                                = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
-                test_genome_vcf_gz                             = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
-                test_genome_vcf_gz_tbi                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
-                test_genome_vcf_idx                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
+                test_genome_vcf                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf"
+                test_genome_vcf_gz                                      = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz"
+                test_genome_vcf_gz_tbi                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz.tbi"
+                test_genome_vcf_idx                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx"
 
-                test2_genome_vcf                               = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
-                test2_genome_vcf_gz                            = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
-                test2_genome_vcf_gz_tbi                        = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
-                test2_genome_vcf_idx                           = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
+                test2_genome_vcf                                        = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf"
+                test2_genome_vcf_gz                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz"
+                test2_genome_vcf_gz_tbi                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi"
+                test2_genome_vcf_idx                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx"
 
-                test_genome21_indels_vcf_gz                    = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
-                test_genome21_indels_vcf_gz_tbi                = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
+                test_genome21_indels_vcf_gz                             = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz"
+                test_genome21_indels_vcf_gz_tbi                         = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi"
 
-                test_mpileup                                   = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
-                test2_mpileup                                  = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
+                test_mpileup                                            = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test.mpileup.gz"
+                test2_mpileup                                           = "${test_data_dir}/genomics/homo_sapiens/illumina/mpileup/test2.mpileup.gz"
 
-                test_broadpeak                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
-                test2_broadpeak                                = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
+                test_broadpeak                                          = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak"
+                test2_broadpeak                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak"
 
-                test_narrowpeak                                = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
-                test2_narrowpeak                               = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
+                test_narrowpeak                                         = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak"
+                test2_narrowpeak                                        = "${test_data_dir}/genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak"
 
-                test_10x_1_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
-                test_10x_2_fastq_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
+                test_10x_1_fastq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R1_001.fastq.gz"
+                test_10x_2_fastq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/10xgenomics/test_10x_S1_L001_R2_001.fastq.gz"
 
-                test_yak                                      = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
-                test2_yak                                     = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
+                test_yak                                                = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test.yak"
+                test2_yak                                               = "${test_data_dir}/genomics/homo_sapiens/illumina/yak/test2.yak"
 
-                cutandrun_bedgraph_test_1                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
-                cutandrun_bedgraph_test_2                     = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
+                cutandrun_bedgraph_test_1                               = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_h3k27me3_test_1.bedGraph"
+                cutandrun_bedgraph_test_2                               = "${test_data_dir}/genomics/homo_sapiens/illumina/bedgraph/cutandtag_igg_test_1.bedGraph"
 
-                test_rnaseq_vcf                               =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
-                test_sv_vcf                                   =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
+                test_rnaseq_vcf                                         =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.rnaseq.vcf"
+                test_sv_vcf                                             =  "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz"
 
-                test_pytor                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
+                test_pytor                                              = "${test_data_dir}/genomics/homo_sapiens/illumina/pytor/test.pytor"
             }
             'pacbio' {
-                primers                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
-                alz                                           = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
-                alzpbi                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
-                ccs                                           = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
-                ccs_fa                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
-                ccs_fa_gz                                     = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
-                ccs_fq                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
-                ccs_fq_gz                                     = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
-                ccs_xml                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
-                hifi                                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
-                lima                                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
-                refine                                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
-                cluster                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
-                singletons                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
-                aligned                                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
-                alignedbai                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
-                genemodel1                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
-                genemodel2                                    = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
-                filelist                                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
+                primers                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/primers.fasta"
+                alz                             = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam"
+                alzpbi                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.bam.pbi"
+                ccs                             = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.bam"
+                ccs_fa                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta"
+                ccs_fa_gz                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fasta/alz.ccs.fasta.gz"
+                ccs_fq                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq"
+                ccs_fq_gz                       = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/alz.ccs.fastq.gz"
+                ccs_xml                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/xml/alz.ccs.consensusreadset.xml"
+                hifi                            = "${test_data_dir}/genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz"
+                lima                            = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.bam"
+                refine                          = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.bam"
+                cluster                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.bam"
+                singletons                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.bam"
+                aligned                         = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam"
+                alignedbai                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/bam/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned.bam.bai"
+                genemodel1                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.bed"
+                genemodel2                      = "${test_data_dir}/genomics/homo_sapiens/pacbio/bed/alz.ccs.fl.NEB_5p--NEB_Clontech_3p.flnc.clustered.singletons.merged.aligned_tc.2.bed"
+                filelist                        = "${test_data_dir}/genomics/homo_sapiens/pacbio/txt/filelist.txt"
             }
         }
         'bacteroides_fragilis' {
@@ -393,31 +394,31 @@ params {
         }
         'generic' {
             'csv' {
-                test_csv = "${test_data_dir}/generic/csv/test.csv"
+                test_csv                        = "${test_data_dir}/generic/csv/test.csv"
             }
             'notebooks' {
-                rmarkdown = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
-                ipython_md = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
-                ipython_ipynb = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
+                rmarkdown                       = "${test_data_dir}/generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd"
+                ipython_md                      = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.md"
+                ipython_ipynb                   = "${test_data_dir}/generic/notebooks/jupyter/ipython_notebook.ipynb"
             }
             'tsv' {
-                test_tsv = "${test_data_dir}/generic/tsv/test.tsv"
+                test_tsv                        = "${test_data_dir}/generic/tsv/test.tsv"
             }
             'txt' {
-                hello = "${test_data_dir}/generic/txt/hello.txt"
+                hello                           = "${test_data_dir}/generic/txt/hello.txt"
             }
             'cnn' {
-                reference = "${test_data_dir}/generic/cnn/reference.cnn"
+                reference                       = "${test_data_dir}/generic/cnn/reference.cnn"
             }
             'cooler'{
-                test_pairix_pair_gz                           = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
-                test_pairix_pair_gz_px2                       = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
-                test_pairs_pair                               = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
-                test_tabix_pair_gz                            = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
-                test_tabix_pair_gz_tbi                        = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
-                hg19_chrom_sizes                              = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
-                test_merge_cool                               = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
-                test_merge_cool_cp2                           = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
+                test_pairix_pair_gz             = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
+                test_pairix_pair_gz_px2         = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
+                test_pairs_pair                 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.sample1.pairs"
+                test_tabix_pair_gz              = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz"
+                test_tabix_pair_gz_tbi          = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.sorted.possrt.txt.gz.tbi"
+                hg19_chrom_sizes                = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.chrom.sizes"
+                test_merge_cool                 = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cool"
+                test_merge_cool_cp2             = "${test_data_dir}/genomics/homo_sapiens/cooler/merge/toy/toy.symm.upper.2.cp2.cool"
 
             }
         }
diff --git a/tests/modules/gatk4/mergebamalignment/main.nf b/tests/modules/gatk4/mergebamalignment/main.nf
index 0eb6876d..d0949a52 100644
--- a/tests/modules/gatk4/mergebamalignment/main.nf
+++ b/tests/modules/gatk4/mergebamalignment/main.nf
@@ -17,11 +17,11 @@ workflow test_gatk4_mergebamalignment {
 
 workflow test_gatk4_mergebamalignment_stubs {
      input    = [ [ id:'test' ], // meta map
-                 "test_foo.bam",
-                 "test_bar.bam"
+                 file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
+                 file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
                ]
-    fasta    = "genome.fasta"
-    dict     = "genome.fasta.dict"
+    fasta    = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    dict     = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
 
     GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
 }
diff --git a/tests/modules/gatk4/mergebamalignment/test.yml b/tests/modules/gatk4/mergebamalignment/test.yml
index 84a67654..01d9bf46 100644
--- a/tests/modules/gatk4/mergebamalignment/test.yml
+++ b/tests/modules/gatk4/mergebamalignment/test.yml
@@ -9,7 +9,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mergebamalignment test_gatk4_mergebamalignment_stubs
-  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/mergebamalignment -entry test_gatk4_mergebamalignment_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergebamalignment/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/mergebamalignment
diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf
index 310e9ca1..fa229eff 100644
--- a/tests/modules/gatk4/mutect2/main.nf
+++ b/tests/modules/gatk4/mutect2/main.nf
@@ -120,23 +120,23 @@ workflow test_gatk4_mutect2_mitochondria {
 }
 
 workflow test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs {
-    input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
-              [ "foo_paired.bam",
-                "foo_paired2.bam"
+     input = [ [ id:'test', normal_id:'normal', tumor_id:'tumour' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)
                 ],
-              [ "foo_paired.bam.bai",
-                "foo_paired2.bam.bai"
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)
                 ],
               []
             ]
 
-    fasta = "genome.fasta"
-    fai = "genome.fasta.fai"
-    dict = "genome.fasta.dict"
-    germline_resource = "genome_gnomAD.r2.1.1.vcf.gz"
-    germline_resource_tbi = "genome_gnomAD.r2.1.1.vcf.gz.tbi"
-    panel_of_normals = "genome_mills_and_1000G.indels.hg38.vcf.gz"
-    panel_of_normals_tbi = "genome_mills_and_1000G.indels.hg38.vcf.gz.tbi"
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+    germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
+    germline_resource_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
+    panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true)
+    panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true)
 
     GATK4_MUTECT2_F1R2 ( input, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi )
 }
diff --git a/tests/modules/gatk4/mutect2/test.yml b/tests/modules/gatk4/mutect2/test.yml
index 3853801d..27fb40b9 100644
--- a/tests/modules/gatk4/mutect2/test.yml
+++ b/tests/modules/gatk4/mutect2/test.yml
@@ -71,7 +71,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 mutect2 test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs
-  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2 -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/mutect2 -entry test_gatk4_mutect2_tumor_normal_pair_f1r2_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mutect2/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/mutect2
diff --git a/tests/modules/gatk4/revertsam/main.nf b/tests/modules/gatk4/revertsam/main.nf
index 738ecd8f..5b14d471 100644
--- a/tests/modules/gatk4/revertsam/main.nf
+++ b/tests/modules/gatk4/revertsam/main.nf
@@ -14,7 +14,7 @@ workflow test_gatk4_revertsam {
 
 workflow test_gatk4_revertsam_stubs {
     input = [ [ id:'test' ], // meta map
-              "foo_paired_end.bam"
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
             ]
 
     GATK4_REVERTSAM ( input )
diff --git a/tests/modules/gatk4/revertsam/test.yml b/tests/modules/gatk4/revertsam/test.yml
index 89e78659..fd26d06f 100644
--- a/tests/modules/gatk4/revertsam/test.yml
+++ b/tests/modules/gatk4/revertsam/test.yml
@@ -9,7 +9,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 revertsam test_gatk4_revertsam_stubs
-  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/revertsam -entry test_gatk4_revertsam_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/revertsam/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/revertsam
diff --git a/tests/modules/gatk4/samtofastq/main.nf b/tests/modules/gatk4/samtofastq/main.nf
index 79d04c7c..757b080f 100644
--- a/tests/modules/gatk4/samtofastq/main.nf
+++ b/tests/modules/gatk4/samtofastq/main.nf
@@ -21,8 +21,8 @@ workflow test_gatk4_samtofastq_paired_end {
 }
 
 workflow test_gatk4_samtofastq_paired_end_stubs {
-    input = [ [ id:'test', single_end: false ], // meta map
-              [ "foo_paired_end.bam" ]
+    input = [ [ id:'test', single_end: true ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ]
             ]
 
     GATK4_SAMTOFASTQ ( input )
diff --git a/tests/modules/gatk4/samtofastq/test.yml b/tests/modules/gatk4/samtofastq/test.yml
index 1288a270..bab7fc7a 100644
--- a/tests/modules/gatk4/samtofastq/test.yml
+++ b/tests/modules/gatk4/samtofastq/test.yml
@@ -21,7 +21,7 @@
     - path: output/gatk4/versions.yml
 
 - name: gatk4 samtofastq test_gatk4_samtofastq_paired_end_stubs
-  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/gatk4/samtofastq -entry test_gatk4_samtofastq_paired_end_stubs -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/samtofastq/nextflow.config -stub-run
   tags:
     - gatk4
     - gatk4/samtofastq
diff --git a/tests/modules/samtools/view/main.nf b/tests/modules/samtools/view/main.nf
index bdad1078..0e3f597e 100644
--- a/tests/modules/samtools/view/main.nf
+++ b/tests/modules/samtools/view/main.nf
@@ -25,7 +25,7 @@ workflow test_samtools_view_cram {
 
 workflow test_samtools_view_stubs {
     input = [ [ id:'test', single_end:false ], // meta map
-                "foo_paired_end.bam",
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
                 []
             ]
 
diff --git a/tests/modules/samtools/view/test.yml b/tests/modules/samtools/view/test.yml
index 2718130e..f3ad4552 100644
--- a/tests/modules/samtools/view/test.yml
+++ b/tests/modules/samtools/view/test.yml
@@ -16,7 +16,7 @@
     - path: output/samtools/test.cram
 
 - name: samtools view test_samtools_view_stubs
-  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
+  command: nextflow run ./tests/modules/samtools/view -entry test_samtools_view_stubs -c ./tests/config/nextflow.config -c ./tests/modules/samtools/view/nextflow.config -stub-run
   tags:
     - samtools/view
     - samtools
diff --git a/tests/modules/snapaligner/align/main.nf b/tests/modules/snapaligner/align/main.nf
new file mode 100644
index 00000000..4f5943fe
--- /dev/null
+++ b/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 )
+}
diff --git a/tests/modules/snapaligner/paired/nextflow.config b/tests/modules/snapaligner/align/nextflow.config
similarity index 100%
rename from tests/modules/snapaligner/paired/nextflow.config
rename to tests/modules/snapaligner/align/nextflow.config
diff --git a/tests/modules/snapaligner/align/test.yml b/tests/modules/snapaligner/align/test.yml
new file mode 100644
index 00000000..4e4fae61
--- /dev/null
+++ b/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
diff --git a/tests/modules/snapaligner/paired/main.nf b/tests/modules/snapaligner/paired/main.nf
deleted file mode 100644
index b25ca8c2..00000000
--- a/tests/modules/snapaligner/paired/main.nf
+++ /dev/null
@@ -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 )
-}
diff --git a/tests/modules/snapaligner/paired/test.yml b/tests/modules/snapaligner/paired/test.yml
deleted file mode 100644
index 7df1e02b..00000000
--- a/tests/modules/snapaligner/paired/test.yml
+++ /dev/null
@@ -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
diff --git a/tests/modules/snapaligner/single/main.nf b/tests/modules/snapaligner/single/main.nf
deleted file mode 100644
index 616e517a..00000000
--- a/tests/modules/snapaligner/single/main.nf
+++ /dev/null
@@ -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 )
-}
diff --git a/tests/modules/snapaligner/single/nextflow.config b/tests/modules/snapaligner/single/nextflow.config
deleted file mode 100644
index 50f50a7a..00000000
--- a/tests/modules/snapaligner/single/nextflow.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
diff --git a/tests/modules/snapaligner/single/test.yml b/tests/modules/snapaligner/single/test.yml
deleted file mode 100644
index bbcbba1f..00000000
--- a/tests/modules/snapaligner/single/test.yml
+++ /dev/null
@@ -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
diff --git a/tests/subworkflows/nf-core/annotation/snpeff/main.nf b/tests/subworkflows/nf-core/annotation/snpeff/main.nf
index 4aee20ee..bb56b46b 100644
--- a/tests/subworkflows/nf-core/annotation/snpeff/main.nf
+++ b/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 = [