diff --git a/modules/antismash/antismashlitedownloaddatabases/main.nf b/modules/antismash/antismashlitedownloaddatabases/main.nf
index 1853d80a..72314eee 100644
--- a/modules/antismash/antismashlitedownloaddatabases/main.nf
+++ b/modules/antismash/antismashlitedownloaddatabases/main.nf
@@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
         'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
 
     /*
-    These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
+    These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
     Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
+    These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
     */
 
     containerOptions {
@@ -26,6 +27,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     output:
     path("antismash_db") , emit: database
+    path("css"), emit: css_dir
+    path("detection"), emit: detection_dir
+    path("modules"), emit: modules_dir
     path "versions.yml", emit: versions
 
     when:
@@ -40,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        antismash: \$(antismash --version | sed 's/antiSMASH //')
+        antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
     END_VERSIONS
     """
 }
diff --git a/modules/antismash/antismashlitedownloaddatabases/meta.yml b/modules/antismash/antismashlitedownloaddatabases/meta.yml
index ad393bae..619dc8c2 100644
--- a/modules/antismash/antismashlitedownloaddatabases/meta.yml
+++ b/modules/antismash/antismashlitedownloaddatabases/meta.yml
@@ -27,17 +27,17 @@ input:
   - database_css:
       type: directory
       description: |
-        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "css"
   - database_detection:
       type: directory
       description: |
-        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "detection"
   - database_modules:
       type: directory
       description: |
-        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
       pattern: "modules"
 
 output:
@@ -50,6 +50,21 @@ output:
       type: directory
       description: Download directory for antiSMASH databases
       pattern: "antismash_db"
+  - css_dir:
+      type: directory
+      description: |
+        antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "css"
+  - detection_dir:
+      type: directory
+      description: |
+        antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "detection"
+  - modules_dir:
+      type: directory
+      description: |
+        antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
+      pattern: "modules"
 
 authors:
   - "@jasmezz"
diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf
index bf0877c3..b6854895 100644
--- a/modules/cat/fastq/main.nf
+++ b/modules/cat/fastq/main.nf
@@ -4,8 +4,8 @@ process CAT_FASTQ {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
diff --git a/modules/custom/getchromsizes/main.nf b/modules/custom/getchromsizes/main.nf
index bbcfa9be..0eabf3a4 100644
--- a/modules/custom/getchromsizes/main.nf
+++ b/modules/custom/getchromsizes/main.nf
@@ -2,10 +2,10 @@ process CUSTOM_GETCHROMSIZES {
     tag "$fasta"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
 
     input:
     path fasta
diff --git a/modules/gamma/main.nf b/modules/gamma/main.nf
new file mode 100644
index 00000000..e176ee68
--- /dev/null
+++ b/modules/gamma/main.nf
@@ -0,0 +1,41 @@
+def VERSION = '2.1' // Version information not provided by tool on CLI
+
+process GAMMA {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
+        'quay.io/biocontainers/gamma:2.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fasta)
+    path(db)
+
+    output:
+    tuple val(meta), path("*.gamma")                , emit: gamma
+    tuple val(meta), path("*.psl")                  , emit: psl
+    tuple val(meta), path("*.gff")  , optional:true , emit: gff
+    tuple val(meta), path("*.fasta"), optional:true , emit: fasta
+    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}"
+    """
+    GAMMA.py \\
+        $args \\
+        $fasta \\
+        $db \\
+        $prefix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gamma: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/gamma/meta.yml b/modules/gamma/meta.yml
new file mode 100644
index 00000000..316b685b
--- /dev/null
+++ b/modules/gamma/meta.yml
@@ -0,0 +1,63 @@
+name: "gamma"
+description: Gene Allele Mutation Microbial Assessment
+keywords:
+  - gamma
+  - gene-calling
+tools:
+  - "gamma":
+      description: "Tool for Gene Allele Mutation Microbial Assessment"
+      homepage: "https://github.com/rastanton/GAMMA"
+      documentation: "https://github.com/rastanton/GAMMA"
+      tool_dev_url: "https://github.com/rastanton/GAMMA"
+      doi: "10.1093/bioinformatics/btab607"
+      licence: "['Apache License 2.0']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: FASTA file
+      pattern: "*.{fa,fasta}"
+  - db:
+      type: file
+      description: Database in FASTA format
+      pattern: "*.{fa,fasta}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - gamma:
+      type: file
+      description: GAMMA file with annotated gene matches
+      pattern: "*.{gamma}"
+
+  - psl:
+      type: file
+      description: PSL file with all gene matches found
+      pattern: "*.{psl}"
+
+  - gff:
+      type: file
+      description: GFF file
+      pattern: "*.{gff}"
+
+  - fasta:
+      type: file
+      description: multifasta file of the gene matches
+      pattern: "*.{fasta}"
+
+authors:
+  - "@sateeshperi"
+  - "@rastanton"
diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf
index f7c559d9..85e5daa8 100644
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@@ -8,7 +8,7 @@ process GATK4_SPLITNCIGARREADS {
         'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bam), path(bai), path(intervals)
     path  fasta
     path  fai
     path  dict
@@ -23,6 +23,7 @@ process GATK4_SPLITNCIGARREADS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def interval_command = intervals ? "--intervals $intervals" : ""
 
     def avail_mem = 3
     if (!task.memory) {
@@ -35,6 +36,7 @@ process GATK4_SPLITNCIGARREADS {
         --input $bam \\
         --output ${prefix}.bam \\
         --reference $fasta \\
+        $interval_command \\
         --tmp-dir . \\
         $args
 
diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml
index 407e80bd..76bfdcd3 100644
--- a/modules/gatk4/splitncigarreads/meta.yml
+++ b/modules/gatk4/splitncigarreads/meta.yml
@@ -23,6 +23,13 @@ input:
       type: list
       description: BAM/SAM/CRAM file containing reads
       pattern: "*.{bam,sam,cram}"
+  - bai:
+      type: list
+      description: BAI/SAI/CRAI index file (optional)
+      pattern: "*.{bai,sai,crai}"
+  - intervals:
+      type: file
+      description: Bed file with the genomic regions included in the library (optional)
   - fasta:
       type: file
       description: The reference fasta file
diff --git a/modules/gunzip/main.nf b/modules/gunzip/main.nf
index 9d4b0666..61bf1afa 100644
--- a/modules/gunzip/main.nf
+++ b/modules/gunzip/main.nf
@@ -4,8 +4,8 @@ process GUNZIP {
 
     conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
-        'biocontainers/biocontainers:v1.2.0_cv1' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)
diff --git a/modules/minimap2/align/main.nf b/modules/minimap2/align/main.nf
index fe06f14d..7ba05ee9 100644
--- a/modules/minimap2/align/main.nf
+++ b/modules/minimap2/align/main.nf
@@ -2,18 +2,22 @@ process MINIMAP2_ALIGN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
+    conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
-        'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
+        'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
 
     input:
     tuple val(meta), path(reads)
     path reference
+    val bam_format
+    val cigar_paf_format
+    val cigar_bam
 
     output:
-    tuple val(meta), path("*.paf"), emit: paf
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.paf"), optional: true, emit: paf
+    tuple val(meta), path("*.bam"), optional: true, emit: bam
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
+    def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
+    def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
+    def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
     """
     minimap2 \\
         $args \\
         -t $task.cpus \\
         $reference \\
         $input_reads \\
-        > ${prefix}.paf
+        $cigar_paf \\
+        $set_cigar_bam \\
+        $bam_output
+
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml
index 89e24283..991b39a0 100644
--- a/modules/minimap2/align/meta.yml
+++ b/modules/minimap2/align/meta.yml
@@ -29,6 +29,17 @@ input:
       type: file
       description: |
         Reference database in FASTA format.
+  - bam_format:
+      type: boolean
+      description: Specify that output should be in BAM format
+  - cigar_paf_format:
+      type: boolean
+      description: Specify that output CIGAR should be in PAF format
+  - cigar_bam:
+      type: boolean
+      description: |
+        Write CIGAR with >65535 ops at the CG tag. This is recommended when
+        doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
 output:
   - meta:
       type: map
@@ -39,9 +50,16 @@ output:
       type: file
       description: Alignment in PAF format
       pattern: "*.paf"
+  - bam:
+      type: file
+      description: Alignment in BAM format
+      pattern: "*.bam"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
 authors:
   - "@heuermh"
+  - "@sofstam"
+  - "@sateeshperi"
+  - "@jfy133"
diff --git a/modules/phantompeakqualtools/main.nf b/modules/phantompeakqualtools/main.nf
index f584cb65..d8f73342 100644
--- a/modules/phantompeakqualtools/main.nf
+++ b/modules/phantompeakqualtools/main.nf
@@ -22,11 +22,12 @@ process PHANTOMPEAKQUALTOOLS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args   = task.ext.args ?: ''
+    def args2  = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     RUN_SPP=`which run_spp.R`
-    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
+    Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/rsem/calculateexpression/main.nf b/modules/rsem/calculateexpression/main.nf
index cf147a63..1ab3a635 100644
--- a/modules/rsem/calculateexpression/main.nf
+++ b/modules/rsem/calculateexpression/main.nf
@@ -2,10 +2,10 @@ process RSEM_CALCULATEEXPRESSION {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/rsem/preparereference/main.nf b/modules/rsem/preparereference/main.nf
index 2d2ca205..da11be45 100644
--- a/modules/rsem/preparereference/main.nf
+++ b/modules/rsem/preparereference/main.nf
@@ -2,10 +2,10 @@ process RSEM_PREPAREREFERENCE {
     tag "$fasta"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.6a" : null)
+    conda (params.enable_conda ? "bioconda::rsem=1.3.3 bioconda::star=2.7.10a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' :
-        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:606b713ec440e799d53a2b51a6e79dbfd28ecf3e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' :
+        'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' }"
 
     input:
     path fasta, stageAs: "rsem/*"
diff --git a/modules/samtools/bamtocram/main.nf b/modules/samtools/bamtocram/main.nf
new file mode 100644
index 00000000..b49c308f
--- /dev/null
+++ b/modules/samtools/bamtocram/main.nf
@@ -0,0 +1,35 @@
+//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
+process SAMTOOLS_BAMTOCRAM {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
+        'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
+
+    input:
+    tuple val(meta), path(input), path(index)
+    path  fasta
+    path  fai
+
+    output:
+    tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
+    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}"
+    """
+    samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
+    samtools index -@${task.cpus} ${prefix}.cram
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/samtools/bamtocram/meta.yml b/modules/samtools/bamtocram/meta.yml
new file mode 100644
index 00000000..037704c6
--- /dev/null
+++ b/modules/samtools/bamtocram/meta.yml
@@ -0,0 +1,52 @@
+name: samtools_bamtocram
+description: filter/convert and then index CRAM file
+keywords:
+  - view
+  - index
+  - bam
+  - cram
+tools:
+  - samtools:
+      description: |
+        SAMtools is a set of utilities for interacting with and post-processing
+        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+        These files are generated as output by short read aligners like BWA.
+      homepage: http://www.htslib.org/
+      documentation: hhttp://www.htslib.org/doc/samtools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: file
+      description: BAM/SAM file
+      pattern: "*.{bam,sam}"
+  - index:
+      type: file
+      description: BAM/SAM index file
+      pattern: "*.{bai,sai}"
+  - fasta:
+      type: file
+      description: Reference file to create the CRAM file
+      pattern: "*.{fasta,fa}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - cram_crai:
+      type: file
+      description: filtered/converted CRAM file + index
+      pattern: "*{.cram,.crai}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+  - "@FriederikeHanssen"
+  - "@maxulysse"
diff --git a/modules/stringtie/merge/main.nf b/modules/stringtie/merge/main.nf
index aa11eb36..c8460c94 100644
--- a/modules/stringtie/merge/main.nf
+++ b/modules/stringtie/merge/main.nf
@@ -2,10 +2,10 @@ process STRINGTIE_MERGE {
     label 'process_medium'
 
     // Note: 2.7X indices incompatible with AWS iGenomes.
-    conda     (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda     (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
 
     input:
     path stringtie_gtf
diff --git a/modules/stringtie/stringtie/main.nf b/modules/stringtie/stringtie/main.nf
index f37e347a..c70c9819 100644
--- a/modules/stringtie/stringtie/main.nf
+++ b/modules/stringtie/stringtie/main.nf
@@ -1,11 +1,11 @@
-process STRINGTIE {
+process STRINGTIE_STRINGTIE {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::stringtie=2.1.7" : null)
+    conda (params.enable_conda ? "bioconda::stringtie=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stringtie:2.1.7--h978d192_0' :
-        'quay.io/biocontainers/stringtie:2.1.7--h978d192_0' }"
+        'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/stringtie:2.2.1--hecb563c_2' }"
 
     input:
     tuple val(meta), path(bam)
diff --git a/modules/stringtie/stringtie/meta.yml b/modules/stringtie/stringtie/meta.yml
index a462c574..0dda84d0 100644
--- a/modules/stringtie/stringtie/meta.yml
+++ b/modules/stringtie/stringtie/meta.yml
@@ -1,4 +1,4 @@
-name: stringtie
+name: stringtie_stringtie
 description: Transcript assembly and quantification for RNA-Se
 keywords:
   - transcript
diff --git a/modules/trimgalore/main.nf b/modules/trimgalore/main.nf
index 9487c799..3a3fca90 100644
--- a/modules/trimgalore/main.nf
+++ b/modules/trimgalore/main.nf
@@ -11,12 +11,13 @@ process TRIMGALORE {
     tuple val(meta), path(reads)
 
     output:
-    tuple val(meta), path("*.fq.gz")    , emit: reads
-    tuple val(meta), path("*report.txt"), emit: log
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*{trimmed,val}*.fq.gz"), emit: reads
+    tuple val(meta), path("*report.txt")          , emit: log
+    path "versions.yml"                           , emit: versions
 
-    tuple val(meta), path("*.html"), emit: html optional true
-    tuple val(meta), path("*.zip") , emit: zip optional true
+    tuple val(meta), path("*unpaired*.fq.gz")     , emit: unpaired, optional: true
+    tuple val(meta), path("*.html")               , emit: html    , optional: true
+    tuple val(meta), path("*.zip")                , emit: zip     , optional: true
 
     when:
     task.ext.when == null || task.ext.when
@@ -52,6 +53,7 @@ process TRIMGALORE {
             $c_r1 \\
             $tpc_r1 \\
             ${prefix}.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
@@ -73,6 +75,7 @@ process TRIMGALORE {
             $tpc_r2 \\
             ${prefix}_1.fastq.gz \\
             ${prefix}_2.fastq.gz
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             trimgalore: \$(echo \$(trim_galore --version 2>&1) | sed 's/^.*version //; s/Last.*\$//')
diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml
index e99a8833..439f566d 100644
--- a/modules/trimgalore/meta.yml
+++ b/modules/trimgalore/meta.yml
@@ -37,6 +37,11 @@ output:
         List of input adapter trimmed FastQ files of size 1 and 2 for
         single-end and paired-end data, respectively.
       pattern: "*.{fq.gz}"
+  - unpaired:
+      type: file
+      description: |
+        FastQ files containing unpaired reads from read 1 or read 2
+      pattern: "*unpaired*.fq.gz"
   - html:
       type: file
       description: FastQC report (optional)
diff --git a/modules/untar/main.nf b/modules/untar/main.nf
index bbfa0bfe..058d1764 100644
--- a/modules/untar/main.nf
+++ b/modules/untar/main.nf
@@ -2,10 +2,10 @@ process UNTAR {
     tag "$archive"
     label 'process_low'
 
-    conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
+    conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
-        'biocontainers/biocontainers:v1.2.0_cv2' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(archive)
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a1a969e7..4d8ce0b5 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -675,6 +675,10 @@ freebayes:
   - modules/freebayes/**
   - tests/modules/freebayes/**
 
+gamma:
+  - modules/gamma/**
+  - tests/modules/gamma/**
+
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**
   - tests/modules/gatk4/applybqsr/**
@@ -1591,6 +1595,10 @@ samtools/bam2fq:
   - modules/samtools/bam2fq/**
   - tests/modules/samtools/bam2fq/**
 
+samtools/bamtocram:
+  - modules/samtools/bamtocram/**
+  - tests/modules/samtools/bamtocram/**
+
 samtools/collatefastq:
   - modules/samtools/collatefastq/**
   - tests/modules/samtools/collatefastq/**
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 559c0d6f..b3171a51 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -245,8 +245,8 @@ params {
                 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                         = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.rnaseq_2.fastq.gz"
+                test_rnaseq_1_fastq_gz                         = "${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"
@@ -335,6 +335,7 @@ params {
         'bacteroides_fragilis' {
             'genome' {
                 genome_fna_gz                   = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz"
+                genome_gbff_gz                  = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.gbff.gz"
                 genome_paf                      = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf"
                 genome_mapping_potential_arg    = "${test_data_dir}/genomics/prokaryotes/bacteroides_fragilis/genome/genome.mapping.potential.ARG"
 
diff --git a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
index 3493bb4b..1079363c 100644
--- a/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
+++ b/tests/modules/antismash/antismashlitedownloaddatabases/test.yml
@@ -1,14 +1,17 @@
 - name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
   command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
   tags:
-    - antismash/antismashlitedownloaddatabases
     - antismash
+    - antismash/antismashlitedownloaddatabases
   files:
     - path: output/antismash/versions.yml
-      md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
+      md5sum: 24859c67023abab99de295d3675a24b6
     - path: output/antismash/antismash_db
     - path: output/antismash/antismash_db/clusterblast
     - path: output/antismash/antismash_db/clustercompare
     - path: output/antismash/antismash_db/pfam
     - path: output/antismash/antismash_db/resfam
     - path: output/antismash/antismash_db/tigrfam
+    - path: output/antismash/css
+    - path: output/antismash/detection
+    - path: output/antismash/modules
diff --git a/tests/modules/gamma/main.nf b/tests/modules/gamma/main.nf
new file mode 100644
index 00000000..f9477706
--- /dev/null
+++ b/tests/modules/gamma/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GAMMA } from '../../../modules/gamma/main.nf'
+
+workflow test_gamma {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    ]
+
+    db = [ file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
+
+    GAMMA ( input, db )
+}
diff --git a/tests/modules/gamma/nextflow.config b/tests/modules/gamma/nextflow.config
new file mode 100644
index 00000000..bbbf4de0
--- /dev/null
+++ b/tests/modules/gamma/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    ext.args = '--fasta'
+
+}
diff --git a/tests/modules/gamma/test.yml b/tests/modules/gamma/test.yml
new file mode 100644
index 00000000..1b493b49
--- /dev/null
+++ b/tests/modules/gamma/test.yml
@@ -0,0 +1,13 @@
+- name: gamma test_gamma
+  command: nextflow run tests/modules/gamma -entry test_gamma -c tests/config/nextflow.config
+  tags:
+    - gamma
+  files:
+    - path: output/gamma/test.fasta
+      md5sum: df37b48466181311e0a679f3c5878484
+    - path: output/gamma/test.gamma
+      md5sum: 3256708fa517a65ed01d99e0e3c762ae
+    - path: output/gamma/test.psl
+      md5sum: 162a2757ed3b167ae1e0cdb24213f940
+    - path: output/gamma/versions.yml
+      md5sum: 3fefb5b46c94993362243c5f9a472057
diff --git a/tests/modules/gatk4/splitncigarreads/main.nf b/tests/modules/gatk4/splitncigarreads/main.nf
index 7e5b7c9a..31e45cec 100644
--- a/tests/modules/gatk4/splitncigarreads/main.nf
+++ b/tests/modules/gatk4/splitncigarreads/main.nf
@@ -6,7 +6,23 @@ include { GATK4_SPLITNCIGARREADS } from '../../../../modules/gatk4/splitncigarre
 
 workflow test_gatk4_splitncigarreads {
     input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ] 
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
+                [],
+                []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_SPLITNCIGARREADS ( input, fasta, fai, dict )
+}
+
+workflow test_gatk4_splitncigarreads_intervals {
+    input = [ [ id:'test' ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+                file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
     fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml
index c38064e2..d9a58901 100644
--- a/tests/modules/gatk4/splitncigarreads/test.yml
+++ b/tests/modules/gatk4/splitncigarreads/test.yml
@@ -5,5 +5,14 @@
     - gatk4/splitncigarreads
   files:
     - path: output/gatk4/test.bam
-      md5sum: ceed15c0bd64ff5c38d3816905933b0b
+      md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
+    - path: output/gatk4/versions.yml
+- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
+  command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
+  tags:
+    - gatk4
+    - gatk4/splitncigarreads
+  files:
+    - path: output/gatk4/test.bam
+      md5sum: cd56e3225950f519fd47164cca60a0bb
     - path: output/gatk4/versions.yml
diff --git a/tests/modules/minimap2/align/main.nf b/tests/modules/minimap2/align/main.nf
index e507d3e5..ee6c0838 100644
--- a/tests/modules/minimap2/align/main.nf
+++ b/tests/modules/minimap2/align/main.nf
@@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
 }
 
 workflow test_minimap2_align_paired_end {
@@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    bam_format  = true
+    cigar_paf_format = false
+    cigar_bam = false
 
-    MINIMAP2_ALIGN ( input, fasta )
+    MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
 }
diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml
index 73dd73e2..c392e313 100644
--- a/tests/modules/minimap2/align/test.yml
+++ b/tests/modules/minimap2/align/test.yml
@@ -1,17 +1,17 @@
-- name: minimap2 align single-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_single_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
 
-- name: minimap2 align paired-end
-  command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
+- name: minimap2 align test_minimap2_align_paired_end
+  command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
   tags:
     - minimap2
     - minimap2/align
   files:
-    - path: ./output/minimap2/test.paf
-      md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
+    - path: output/minimap2/test.bam
+    - path: output/minimap2/versions.yml
diff --git a/tests/modules/rsem/calculateexpression/test.yml b/tests/modules/rsem/calculateexpression/test.yml
index f19c3398..b0251de9 100644
--- a/tests/modules/rsem/calculateexpression/test.yml
+++ b/tests/modules/rsem/calculateexpression/test.yml
@@ -42,7 +42,7 @@
     - path: output/rsem/rsem/genome.transcripts.fa
       md5sum: 050c521a2719c2ae48267c1e65218f29
     - path: output/rsem/rsem/genomeParameters.txt
-      md5sum: 2fe3a030e1706c3e8cd4df3818e6dd2f
+      md5sum: df5a456e3242520cc36e0083a6a7d9dd
     - path: output/rsem/rsem/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
     - path: output/rsem/rsem/sjdbList.fromGTF.out.tab
@@ -63,4 +63,4 @@
     - path: output/rsem/test.stat/test.theta
       md5sum: de2e4490c98cc5383a86ae8225fd0a28
     - path: output/rsem/test.transcript.bam
-      md5sum: 7846491086c478858419667d60f18edd
+      md5sum: ed681d39f5700ffc74d6321525330d93
diff --git a/tests/modules/samtools/bamtocram/main.nf b/tests/modules/samtools/bamtocram/main.nf
new file mode 100644
index 00000000..b1743310
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
+
+workflow test_samtools_bamtocram {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+
+    SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
+}
\ No newline at end of file
diff --git a/tests/modules/samtools/bamtocram/nextflow.config b/tests/modules/samtools/bamtocram/nextflow.config
new file mode 100644
index 00000000..8730f1c4
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}
diff --git a/tests/modules/samtools/bamtocram/test.yml b/tests/modules/samtools/bamtocram/test.yml
new file mode 100644
index 00000000..3cb82902
--- /dev/null
+++ b/tests/modules/samtools/bamtocram/test.yml
@@ -0,0 +1,9 @@
+- name: samtools bamtocram test_samtools_bamtocram
+  command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
+  tags:
+    - samtools/bamtocram
+    - samtools
+  files:
+    - path: output/samtools/test.cram
+    - path: output/samtools/test.cram.crai
+    - path: output/samtools/versions.yml
diff --git a/tests/modules/stringtie/merge/main.nf b/tests/modules/stringtie/merge/main.nf
index 7851e755..3fe32902 100644
--- a/tests/modules/stringtie/merge/main.nf
+++ b/tests/modules/stringtie/merge/main.nf
@@ -2,8 +2,8 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE       } from '../../../../modules/stringtie/stringtie/main.nf'
-include { STRINGTIE_MERGE } from '../../../../modules/stringtie/merge/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_MERGE     } from '../../../../modules/stringtie/merge/main.nf'
 
 /*
  * Test with forward strandedness
@@ -15,8 +15,8 @@ workflow test_stringtie_forward_merge {
     ]
     annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
         .out
         .transcript_gtf
         .map { it -> it[1] }
@@ -35,8 +35,8 @@ workflow test_stringtie_reverse_merge {
     ]
     annotation_gtf = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
-    STRINGTIE
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE
         .out
         .transcript_gtf
         .map { it -> it[1] }
diff --git a/tests/modules/stringtie/merge/test.yml b/tests/modules/stringtie/merge/test.yml
index 392a1d7c..fca66447 100644
--- a/tests/modules/stringtie/merge/test.yml
+++ b/tests/modules/stringtie/merge/test.yml
@@ -5,7 +5,7 @@
     - stringtie/merge
   files:
     - path: output/stringtie/stringtie.merged.gtf
-      md5sum: 9fab7049ef2eafdea246fc787d1def40
+      md5sum: d959eb2fab0db48ded7275e0a2e83c05
     - path: output/stringtie/test.ballgown/e2t.ctab
       md5sum: 9ae42e056c955a88a883e5e917840d77
     - path: output/stringtie/test.ballgown/e_data.ctab
@@ -17,11 +17,10 @@
     - path: output/stringtie/test.ballgown/t_data.ctab
       md5sum: 92a98902784e7406ffe054d2adbabc7c
     - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 9708811bcefe0f6384293d6f419f3250
+      md5sum: 8bcd8e2730ed3337e2730186dbc184f3
     - path: output/stringtie/test.transcripts.gtf
-      md5sum: 0e42709bfe30c2c7f2574ba664f5fa9f
+      md5sum: a914bd55b68a4b5f607738b17861e362
 
 - name: stringtie merge test_stringtie_reverse_merge
   command: nextflow run ./tests/modules/stringtie/merge -entry test_stringtie_reverse_merge -c ./tests/config/nextflow.config -c ./tests/modules/stringtie/merge/nextflow.config
@@ -30,7 +29,7 @@
     - stringtie/merge
   files:
     - path: output/stringtie/stringtie.merged.gtf
-      md5sum: afc461bb3cbc368f268a7a45c1b54497
+      md5sum: 6da479298d73d5b3216d4e1576a2bdf4
     - path: output/stringtie/test.ballgown/e2t.ctab
       md5sum: 9ae42e056c955a88a883e5e917840d77
     - path: output/stringtie/test.ballgown/e_data.ctab
@@ -42,8 +41,7 @@
     - path: output/stringtie/test.ballgown/t_data.ctab
       md5sum: 92a98902784e7406ffe054d2adbabc7c
     - path: output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/stringtie/test.gene.abundance.txt
-      md5sum: 94b85145d60ab1b80a7f0f6cf08418b0
+      md5sum: f289f41b3ba1b9f0aa05d14408f1a5da
     - path: output/stringtie/test.transcripts.gtf
-      md5sum: 3196e3d50fd461aae6408e0a70acae68
+      md5sum: 9dcdc9577c0fdbb25089eda210267546
diff --git a/tests/modules/stringtie/stringtie/main.nf b/tests/modules/stringtie/stringtie/main.nf
index ae6abe67..463e4b98 100644
--- a/tests/modules/stringtie/stringtie/main.nf
+++ b/tests/modules/stringtie/stringtie/main.nf
@@ -2,7 +2,7 @@
 
 nextflow.enable.dsl = 2
 
-include { STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
+include { STRINGTIE_STRINGTIE } from '../../../../modules/stringtie/stringtie/main.nf'
 //
 // Test with forward strandedness
 //
@@ -13,7 +13,7 @@ workflow test_stringtie_forward {
     ]
     annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }
 
 //
@@ -26,5 +26,5 @@ workflow test_stringtie_reverse {
     ]
     annotation_gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)
 
-    STRINGTIE ( input, annotation_gtf )
+    STRINGTIE_STRINGTIE ( input, annotation_gtf )
 }
diff --git a/tests/modules/stringtie/stringtie/test.yml b/tests/modules/stringtie/stringtie/test.yml
index 732b9fd1..2815ba81 100644
--- a/tests/modules/stringtie/stringtie/test.yml
+++ b/tests/modules/stringtie/stringtie/test.yml
@@ -8,7 +8,6 @@
     - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7d8bce7f2a922e367cedccae7267c22e
     - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 6b4cf69bc03f3f69890f972a0e8b7471
     - path: ./output/stringtie/test.ballgown/i_data.ctab
@@ -30,7 +29,6 @@
     - path: ./output/stringtie/test.gene.abundance.txt
       md5sum: 7385b870b955dae2c2ab78a70cf05cce
     - path: ./output/stringtie/test.coverage.gtf
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: ./output/stringtie/test.ballgown/e_data.ctab
       md5sum: 879b6696029d19c4737b562e9d149218
     - path: ./output/stringtie/test.ballgown/i_data.ctab