diff --git a/modules/nf-core/clustalo/align/environment.yml b/modules/nf-core/clustalo/align/environment.yml
index 1e08e574e37..be1eef95ebf 100644
--- a/modules/nf-core/clustalo/align/environment.yml
+++ b/modules/nf-core/clustalo/align/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::clustalo=1.2.4
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/clustalo/align/main.nf b/modules/nf-core/clustalo/align/main.nf
index f35ed407aad..eb230cad269 100644
--- a/modules/nf-core/clustalo/align/main.nf
+++ b/modules/nf-core/clustalo/align/main.nf
@@ -4,16 +4,17 @@ process CLUSTALO_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/clustalo:1.2.4--h87f3376_5':
-        'biocontainers/clustalo:1.2.4--h87f3376_5' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-4cefc38542f86c17596c29b35a059de10387c6a7:adbe4fbad680f9beb083956d79128039a727e7b3-0':
+        'biocontainers/mulled-v2-4cefc38542f86c17596c29b35a059de10387c6a7:adbe4fbad680f9beb083956d79128039a727e7b3-0' }"
 
     input:
-    tuple val(meta),  path(fasta)
+    tuple val(meta) , path(fasta)
     tuple val(meta2), path(tree)
+    val(compress)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,16 +22,23 @@ process CLUSTALO_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def write_output = compress ? "--force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln"
+    // using >() is necessary to preserve the return value,
+    // so nextflow knows to display an error when it failed
+    // the --force -o is necessary, as clustalo expands the commandline input,
+    // causing it to treat the pipe as a parameter and fail
+    // this way, the command expands to /dev/fd/<id>, and --force allows writing output to an already existing file
     """
-    clustalo \\
-        -i ${fasta} \\
-        --threads=${task.cpus} \\
-        $args \\
-        -o ${prefix}.aln
+    clustalo \
+        -i ${fasta} \
+        --threads=${task.cpus} \
+        $args \
+        $write_output
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         clustalo: \$( clustalo --version )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
@@ -38,11 +46,12 @@ process CLUSTALO_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         clustalo: \$( clustalo --version )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/clustalo/align/meta.yml b/modules/nf-core/clustalo/align/meta.yml
index 639013676bc..469b3a37691 100644
--- a/modules/nf-core/clustalo/align/meta.yml
+++ b/modules/nf-core/clustalo/align/meta.yml
@@ -12,6 +12,10 @@ tools:
       tool_dev_url: "http://www.clustal.org/omega/"
       doi: "10.1038/msb.2011.75"
       licence: ["GPL v2"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 input:
   - meta:
       type: map
@@ -31,6 +35,9 @@ input:
       type: file
       description: Input guide tree in Newick format
       pattern: "*.{dnd}"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
 output:
   - meta:
       type: map
@@ -39,8 +46,8 @@ output:
         e.g. `[ id:'test']`
   - alignment:
       type: file
-      description: Alignment file.
-      pattern: "*.{aln}"
+      description: Alignment file, in gzipped fasta format
+      pattern: "*.aln{.gz,}"
   - versions:
       type: file
       description: File containing software versions
@@ -51,3 +58,4 @@ authors:
 maintainers:
   - "@luisas"
   - "@joseespinosa"
+  - "@lrauschning"
diff --git a/modules/nf-core/clustalo/align/tests/main.nf.test b/modules/nf-core/clustalo/align/tests/main.nf.test
index 849dd5fa127..3edd36a21c0 100644
--- a/modules/nf-core/clustalo/align/tests/main.nf.test
+++ b/modules/nf-core/clustalo/align/tests/main.nf.test
@@ -4,13 +4,38 @@ nextflow_process {
     script "../main.nf"
     process "CLUSTALO_ALIGN"
     config "./nextflow.config"
-    
+
     tag "modules"
     tag "modules_nfcore"
     tag "clustalo"
     tag "clustalo/align"
+    tag "clustalo/guidetree"
+
+    test("sarscov2 - contigs-fasta - uncompressed") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                             file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.alignment).match("alignment - uncompressed")},
+                { assert snapshot(process.out.versions).match("versions0") }
+            )
+        }
+
+    }
 
-    test("sarscov2 - contigs-fasta") {
+    test("sarscov2 - contigs-fasta - compressed") {
 
         when {
             process {
@@ -19,6 +44,7 @@ nextflow_process {
                              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
+                input[2] = true
                 """
             }
         }
@@ -26,8 +52,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment")},
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.alignment).match("alignment - compressed")},
+                { assert snapshot(process.out.versions).match("versions1") }
             )
         }
 
@@ -56,6 +82,7 @@ nextflow_process {
                              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
                            ]
                 input[1] = CLUSTALO_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_summary'], tree]}
+                input[2] = true
                 """
             }
         }
@@ -68,4 +95,4 @@ nextflow_process {
             )
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/clustalo/align/tests/main.nf.test.snap b/modules/nf-core/clustalo/align/tests/main.nf.test.snap
index 976cb5085c3..d7d69870c87 100644
--- a/modules/nf-core/clustalo/align/tests/main.nf.test.snap
+++ b/modules/nf-core/clustalo/align/tests/main.nf.test.snap
@@ -1,13 +1,26 @@
 {
+    "alignment - compressed": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln.gz:md5,74bb9a2820a91cf68db94dbd46787722"
+                ]
+            ]
+        ],
+        "timestamp": "2024-02-09T19:39:46.647351958"
+    },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,67b67f513195c4f7ab9ddadc309135fe"
+                "versions.yml:md5,327da6a4250a6b7c4e45cddaa1f56280"
             ]
         ],
-        "timestamp": "2023-11-27T14:50:24.517805"
+        "timestamp": "2024-02-09T19:39:14.826528498"
     },
-    "with_guide_tree_alignment": {
+    "alignment - uncompressed": {
         "content": [
             [
                 [
@@ -18,27 +31,27 @@
                 ]
             ]
         ],
-        "timestamp": "2023-11-28T16:28:59.20367"
+        "timestamp": "2024-02-09T19:39:14.786480272"
     },
-    "alignment": {
+    "with_guide_tree_alignment": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln:md5,74bb9a2820a91cf68db94dbd46787722"
+                    "test.aln.gz:md5,74bb9a2820a91cf68db94dbd46787722"
                 ]
             ]
         ],
-        "timestamp": "2023-11-27T14:50:24.471198"
+        "timestamp": "2024-02-09T19:40:45.057777867"
     },
     "with_guide_tree_versions": {
         "content": [
             [
-                "versions.yml:md5,67b67f513195c4f7ab9ddadc309135fe"
+                "versions.yml:md5,327da6a4250a6b7c4e45cddaa1f56280"
             ]
         ],
-        "timestamp": "2023-11-28T16:28:59.225509"
+        "timestamp": "2024-02-09T19:40:45.122824595"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/famsa/align/main.nf b/modules/nf-core/famsa/align/main.nf
index 388b133951e..096d8ff3890 100644
--- a/modules/nf-core/famsa/align/main.nf
+++ b/modules/nf-core/famsa/align/main.nf
@@ -10,26 +10,29 @@ process FAMSA_ALIGN {
         'biocontainers/famsa:2.2.2--h9f5acd7_0' }"
 
     input:
-    tuple val(meta),  path(fasta)
+    tuple val(meta) , path(fasta)
     tuple val(meta2), path(tree)
+    val(compress)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def compress_args = compress ? '-gz' : ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def options_tree = tree ? "-gt import $tree" : ""
     """
     famsa $options_tree \\
+        $compress_args \\
         $args \\
         -t ${task.cpus} \\
         ${fasta} \\
-        ${prefix}.aln
+        ${prefix}.aln${compress ? '.gz':''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -40,7 +43,7 @@ process FAMSA_ALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/famsa/align/meta.yml b/modules/nf-core/famsa/align/meta.yml
index 06a66c274f3..6acf3c21010 100644
--- a/modules/nf-core/famsa/align/meta.yml
+++ b/modules/nf-core/famsa/align/meta.yml
@@ -33,6 +33,9 @@ input:
       type: file
       description: Input guide tree in Newick format
       pattern: "*.{dnd}"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args.
 output:
   - meta:
       type: map
@@ -41,8 +44,8 @@ output:
         e.g. `[ id:'test']`
   - alignment:
       type: file
-      description: Alignment file.
-      pattern: "*.{aln}"
+      description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false
+      pattern: "*.aln{.gz,}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/famsa/align/tests/main.nf.test b/modules/nf-core/famsa/align/tests/main.nf.test
index 45bfee267fb..2d7cac3c4e0 100644
--- a/modules/nf-core/famsa/align/tests/main.nf.test
+++ b/modules/nf-core/famsa/align/tests/main.nf.test
@@ -8,8 +8,9 @@ nextflow_process {
     tag "modules_nfcore"
     tag "famsa"
     tag "famsa/align"
+    tag "famsa/guidetree"
 
-    test("sarscov2 - fasta") {
+    test("sarscov2 - fasta - uncompressed") {
 
         when {
             process {
@@ -18,6 +19,7 @@ nextflow_process {
                              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
                            ]
                 input[1] = [[:],[]]
+                input[2] = false
                 """
             }
         }
@@ -25,8 +27,32 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.alignment).match("alignment")},
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.alignment).match("alignment_uncompressed")},
+                { assert snapshot(process.out.versions).match("versions0") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - compressed") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ], // meta map
+                             file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.alignment).match("alignment_compressed")},
+                { assert snapshot(process.out.versions).match("versions1") }
             )
         }
 
@@ -54,6 +80,7 @@ nextflow_process {
                              file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
                            ]
                 input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_summary'], tree]}
+                input[2] = true
                 """
             }
         }
@@ -66,4 +93,4 @@ nextflow_process {
             )
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/famsa/align/tests/main.nf.test.snap b/modules/nf-core/famsa/align/tests/main.nf.test.snap
index f5795e7363e..95bbbf17750 100644
--- a/modules/nf-core/famsa/align/tests/main.nf.test.snap
+++ b/modules/nf-core/famsa/align/tests/main.nf.test.snap
@@ -1,11 +1,24 @@
 {
+    "alignment_uncompressed": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln:md5,7cf7375f2ba360814ea978731838b972"
+                ]
+            ]
+        ],
+        "timestamp": "2024-02-09T19:08:43.577982822"
+    },
     "versions": {
         "content": [
             [
                 "versions.yml:md5,7d9e0a8c263fa6d9017075fe88c9e9dc"
             ]
         ],
-        "timestamp": "2023-11-29T11:45:52.435457374"
+        "timestamp": "2024-02-09T19:08:43.670136799"
     },
     "with_guide_tree_alignment": {
         "content": [
@@ -14,24 +27,24 @@
                     {
                         "id": "test"
                     },
-                    "test.aln:md5,7cf7375f2ba360814ea978731838b972"
+                    "test.aln.gz:md5,7cf7375f2ba360814ea978731838b972"
                 ]
             ]
         ],
-        "timestamp": "2023-11-29T11:46:17.140198556"
+        "timestamp": "2024-02-09T19:10:05.167368314"
     },
-    "alignment": {
+    "alignment_compressed": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln:md5,7cf7375f2ba360814ea978731838b972"
+                    "test.aln.gz:md5,7cf7375f2ba360814ea978731838b972"
                 ]
             ]
         ],
-        "timestamp": "2023-11-29T11:45:52.421966018"
+        "timestamp": "2024-02-09T19:09:25.819156831"
     },
     "with_guide_tree_versions": {
         "content": [
@@ -39,6 +52,6 @@
                 "versions.yml:md5,7d9e0a8c263fa6d9017075fe88c9e9dc"
             ]
         ],
-        "timestamp": "2023-11-29T11:46:17.147997548"
+        "timestamp": "2024-02-09T19:10:05.231995851"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/mafft/environment.yml b/modules/nf-core/mafft/environment.yml
index fff5c9f3599..595252e08c0 100644
--- a/modules/nf-core/mafft/environment.yml
+++ b/modules/nf-core/mafft/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::mafft=7.520
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/mafft/main.nf b/modules/nf-core/mafft/main.nf
index 43c32c98ba0..f09a0c96246 100644
--- a/modules/nf-core/mafft/main.nf
+++ b/modules/nf-core/mafft/main.nf
@@ -4,20 +4,21 @@ process MAFFT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mafft:7.520--h031d066_3':
-        'biocontainers/mafft:7.520--h031d066_3' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-12eba4a074f913c639117640936668f5a6a01da6:425707898cf4f85051b77848be253b88f1d2298a-0':
+        'biocontainers/mulled-v2-12eba4a074f913c639117640936668f5a6a01da6:425707898cf4f85051b77848be253b88f1d2298a-0' }"
 
     input:
-    tuple val(meta),  path(fasta)
+    tuple val(meta) , path(fasta)
     tuple val(meta2), path(add)
     tuple val(meta3), path(addfragments)
     tuple val(meta4), path(addfull)
     tuple val(meta5), path(addprofile)
     tuple val(meta6), path(addlong)
+    val(compress)
 
     output:
-    tuple val(meta), path("*.fas"), emit: fas
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.fas{.gz,}"), emit: fas
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,11 +26,13 @@ process MAFFT {
     script:
     def args         = task.ext.args   ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
-    def add          = add             ? "--add ${add}"                   : ''
-    def addfragments = addfragments    ? "--addfragments ${addfragments}" : ''
-    def addfull      = addfull         ? "--addfull ${addfull}"           : ''
-    def addprofile   = addprofile      ? "--addprofile ${addprofile}"     : ''
-    def addlong      = addlong         ? "--addlong ${addlong}"           : ''
+    def add          = add             ? "--add <(unpigz -cdf ${add})"                   : ''
+    def addfragments = addfragments    ? "--addfragments <(unpigz -cdf ${addfragments})" : ''
+    def addfull      = addfull         ? "--addfull <(unpigz -cdf ${addfull})"           : ''
+    def addprofile   = addprofile      ? "--addprofile <(unpigz -cdf ${addprofile})"     : ''
+    def addlong      = addlong         ? "--addlong <(unpigz -cdf ${addlong})"           : ''
+    def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.fas.gz" : "> ${prefix}.fas"
+    // this will not preserve MAFFTs return value, but mafft crashes when it receives a process substitution
     if ("$fasta" == "${prefix}.fas" ) error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
     mafft \\
@@ -41,11 +44,12 @@ process MAFFT {
         ${addlong} \\
         ${args} \\
         ${fasta} \\
-        > ${prefix}.fas
+        ${write_output}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
@@ -59,11 +63,12 @@ process MAFFT {
     def addlong      = addlong         ? "--addlong ${addlong}"           : ''
     if ("$fasta" == "${prefix}.fas" )  error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    touch ${prefix}.fas
+    touch ${prefix}.fas${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mafft: \$(mafft --version 2>&1 | sed 's/^v//' | sed 's/ (.*)//')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml
index fbe121aa11e..90b9ed39c32 100644
--- a/modules/nf-core/mafft/meta.yml
+++ b/modules/nf-core/mafft/meta.yml
@@ -5,13 +5,17 @@ keywords:
   - msa
   - multiple sequence alignment
 tools:
-  - mafft:
+  - "mafft":
       description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
       homepage: https://mafft.cbrc.jp/alignment/software/
       documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html
       tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html
       doi: "10.1093/nar/gkf436"
       licence: ["BSD"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 input:
   - meta:
       type: map
@@ -20,8 +24,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - fasta:
       type: file
-      description: FASTA file containing the sequences to align
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing the sequences to align. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
   - meta2:
       type: map
       description: |
@@ -29,8 +33,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - add:
       type: file
-      description: FASTA file containing sequences to align to the sequences in `fasta` using `--add`
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
   - meta3:
       type: map
       description: |
@@ -38,8 +42,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - addfragments:
       type: file
-      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
   - meta4:
       type: map
       description: |
@@ -47,8 +51,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - addfull:
       type: file
-      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
   - meta5:
       type: map
       description: |
@@ -56,8 +60,8 @@ input:
         e.g. [ id:'test', single_end:false ]
   - addprofile:
       type: file
-      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
   - meta6:
       type: map
       description: |
@@ -65,8 +69,11 @@ input:
         e.g. [ id:'test', single_end:false ]
   - addlong:
       type: file
-      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`
-      pattern: "*.{fa,fasta}"
+      description: FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed.
+      pattern: "*.{fa,fasta}{.gz,}"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
 output:
   - meta:
       type: map
@@ -79,8 +86,8 @@ output:
       pattern: "versions.yml"
   - fas:
       type: file
-      description: Aligned sequences in FASTA format
-      pattern: "*.{fas}"
+      description: Aligned sequences in FASTA format. May be gzipped or uncompressed.
+      pattern: "*.fas{.gz,}"
 authors:
   - "@MillironX"
 maintainers:
diff --git a/modules/nf-core/mafft/tests/main.nf.test b/modules/nf-core/mafft/tests/main.nf.test
index f622724e20e..f57ab4965da 100644
--- a/modules/nf-core/mafft/tests/main.nf.test
+++ b/modules/nf-core/mafft/tests/main.nf.test
@@ -7,7 +7,7 @@ nextflow_process {
     tag "modules_nfcore"
     tag "mafft"
 
-    test("SARS-CoV-2 scaffolds fasta") {
+    test("SARS-CoV-2 scaffolds fasta - uncompressed") {
         when {
             process {
                 """
@@ -20,6 +20,7 @@ nextflow_process {
                 input[3] = [[:], []]
                 input[4] = [[:], []]
                 input[5] = [[:], []]
+                input[6] = false
                 """
             }
         }
@@ -27,7 +28,34 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta")}
+                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - uncompressed")}
+            )
+        }
+
+    }
+
+    test("SARS-CoV-2 scaffolds fasta - compressed") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                        file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+                    ]
+                input[1] = [[:], []]
+                input[2] = [[:], []]
+                input[3] = [[:], []]
+                input[4] = [[:], []]
+                input[5] = [[:], []]
+                input[6] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta - compressed")}
             )
         }
 
@@ -49,6 +77,7 @@ nextflow_process {
                 input[3] = [[:], []]
                 input[4] = [[:], []]
                 input[5] = [[:], []]
+                input[6] = true
                 """
             }
         }
@@ -78,6 +107,7 @@ nextflow_process {
                 input[3] = [[:], []]
                 input[4] = [[:], []]
                 input[5] = [[:], []]
+                input[6] = true
                 """
             }
         }
@@ -106,6 +136,7 @@ nextflow_process {
                     ]
                 input[4] = [[:], []]
                 input[5] = [[:], []]
+                input[6] = true
                 """
             }
         }
@@ -135,6 +166,7 @@ nextflow_process {
                         file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true)
                     ]
                 input[5] = [[:], []]
+                input[6] = true
                 """
             }
         }
@@ -165,6 +197,7 @@ nextflow_process {
                     [ id:'test', single_end:false ], // meta map
                         file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true)
                     ]
+                input[6] = true
                 """
             }
         }
@@ -198,6 +231,7 @@ nextflow_process {
                 input[3] = [[:], []]
                 input[4] = [[:], []]
                 input[5] = [[:], []]
+                input[6] = true
                 """
             }
         }
@@ -211,4 +245,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/mafft/tests/main.nf.test.snap b/modules/nf-core/mafft/tests/main.nf.test.snap
index ebf00f7d393..c14ad086fa1 100644
--- a/modules/nf-core/mafft/tests/main.nf.test.snap
+++ b/modules/nf-core/mafft/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "SARS-CoV-2 scaffolds fasta": {
+    "SARS-CoV-2 scaffolds fasta - uncompressed": {
         "content": [
             {
                 "0": [
@@ -12,7 +12,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -24,137 +24,13 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:31:46.463322875"
+        "timestamp": "2024-02-09T19:08:41.735774847"
     },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta normal": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,a57a34f1c566dea114dc1b13416536d4"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ],
-                "fas": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,a57a34f1c566dea114dc1b13416536d4"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-17T15:39:41.739290654"
-    },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta long": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,e8868da70d1f3050a8daaee0e53b2fd9"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ],
-                "fas": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,e8868da70d1f3050a8daaee0e53b2fd9"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-17T15:40:47.75559372"
-    },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta profile": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,c2b5caf39beff4473878e6aa4036ad43"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ],
-                "fas": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,c2b5caf39beff4473878e6aa4036ad43"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-17T15:40:33.934616343"
-    },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta fragments": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ],
-                "fas": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-17T15:40:05.528308049"
-    },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta full": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta multiple": {
         "content": [
             {
                 "0": [
@@ -163,11 +39,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,611cb0a65195a282f110f7f56e310c66"
+                        "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -175,17 +51,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,611cb0a65195a282f110f7f56e310c66"
+                        "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:40:20.088737531"
+        "timestamp": "2024-02-09T19:10:38.940555785"
     },
-    "SARS-CoV-2 scaffolds fasta - add full": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta normal": {
         "content": [
             {
                 "0": [
@@ -194,11 +70,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,611cb0a65195a282f110f7f56e310c66"
+                        "test.fas.gz:md5,a57a34f1c566dea114dc1b13416536d4"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -206,17 +82,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,611cb0a65195a282f110f7f56e310c66"
+                        "test.fas.gz:md5,a57a34f1c566dea114dc1b13416536d4"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:36:41.023632311"
+        "timestamp": "2024-02-09T19:09:35.656248409"
     },
-    "SARS-CoV-2 scaffolds fasta - add fragments": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta long": {
         "content": [
             {
                 "0": [
@@ -225,11 +101,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
+                        "test.fas.gz:md5,e8868da70d1f3050a8daaee0e53b2fd9"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -237,17 +113,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
+                        "test.fas.gz:md5,e8868da70d1f3050a8daaee0e53b2fd9"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:36:20.211074168"
+        "timestamp": "2024-02-09T19:10:26.372655394"
     },
-    "SARS-CoV-2 scaffolds fasta - add normal": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta profile": {
         "content": [
             {
                 "0": [
@@ -256,11 +132,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,a57a34f1c566dea114dc1b13416536d4"
+                        "test.fas.gz:md5,c2b5caf39beff4473878e6aa4036ad43"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -268,17 +144,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,a57a34f1c566dea114dc1b13416536d4"
+                        "test.fas.gz:md5,c2b5caf39beff4473878e6aa4036ad43"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:36:06.708296829"
+        "timestamp": "2024-02-09T19:10:14.039053212"
     },
-    "SARS-CoV-2 scaffolds fasta - add informative sites fasta multiple": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta fragments": {
         "content": [
             {
                 "0": [
@@ -287,11 +163,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
+                        "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -299,17 +175,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,aed7f866c3a20dc9d2f2b4ad73515961"
+                        "test.fas.gz:md5,aed7f866c3a20dc9d2f2b4ad73515961"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:44:19.543603564"
+        "timestamp": "2024-02-09T19:09:49.737364197"
     },
-    "SARS-CoV-2 scaffolds fasta - add profile": {
+    "SARS-CoV-2 scaffolds fasta - add informative sites fasta full": {
         "content": [
             {
                 "0": [
@@ -318,11 +194,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,c2b5caf39beff4473878e6aa4036ad43"
+                        "test.fas.gz:md5,611cb0a65195a282f110f7f56e310c66"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -330,17 +206,17 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,c2b5caf39beff4473878e6aa4036ad43"
+                        "test.fas.gz:md5,611cb0a65195a282f110f7f56e310c66"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:36:53.336352899"
+        "timestamp": "2024-02-09T19:10:02.952480822"
     },
-    "SARS-CoV-2 scaffolds fasta - add long": {
+    "SARS-CoV-2 scaffolds fasta - compressed": {
         "content": [
             {
                 "0": [
@@ -349,11 +225,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,e8868da70d1f3050a8daaee0e53b2fd9"
+                        "test.fas.gz:md5,23426611f4a0df532b6708f072bd445b"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ],
                 "fas": [
                     [
@@ -361,14 +237,14 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.fas:md5,e8868da70d1f3050a8daaee0e53b2fd9"
+                        "test.fas.gz:md5,23426611f4a0df532b6708f072bd445b"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b505d3a7cf3cd5d0e6a5e4d2944df9b7"
+                    "versions.yml:md5,6e930f6a5acc19ff3a7849536a9fd0ee"
                 ]
             }
         ],
-        "timestamp": "2023-11-17T15:37:15.058221937"
+        "timestamp": "2024-02-09T19:09:21.096197597"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/mtmalign/align/environment.yml b/modules/nf-core/mtmalign/align/environment.yml
index 1cc49c894d5..59d426bb597 100644
--- a/modules/nf-core/mtmalign/align/environment.yml
+++ b/modules/nf-core/mtmalign/align/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::mtm-align=20220104
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/mtmalign/align/main.nf b/modules/nf-core/mtmalign/align/main.nf
index 40254dea85d..c6ad07b7c6d 100644
--- a/modules/nf-core/mtmalign/align/main.nf
+++ b/modules/nf-core/mtmalign/align/main.nf
@@ -6,16 +6,17 @@ process MTMALIGN_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mtm-align:20220104--h4ac6f70_0':
-        'biocontainers/mtm-align:20220104--h4ac6f70_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-5bcf71dc66dac33d8e003c5e78043b80f5c7f269:8f0e486d46f7ab38892c1a8f78d2894a549d03b5-0':
+        'biocontainers/mulled-v2-5bcf71dc66dac33d8e003c5e78043b80f5c7f269:8f0e486d46f7ab38892c1a8f78d2894a549d03b5-0' }"
 
     input:
     tuple val(meta), path('*.pdb', arity: '2..*')
+    val(compress)
 
     output:
-    tuple val(meta), path("./mTM_result/${prefix}.aln")  , emit: alignment
-    tuple val(meta), path("./mTM_result/${prefix}.pdb")    , emit: structure
-    path "versions.yml"                                 , emit: versions
+    tuple val(meta), path("./mTM_result/${prefix}.aln${compress ? '.gz' : ''}"), emit: alignment
+    tuple val(meta), path("./mTM_result/${prefix}.pdb${compress ? '.gz' : ''}"), emit: structure
+    path "versions.yml"                                                        , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,16 +24,32 @@ process MTMALIGN_ALIGN {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    // mTMalign is not capable of writing to stdout
+    // if -o /dev/stdout is specified, the output file will be polluted with debug messages emitted by mTMalign
     """
+    # decompress input files if required
+    if ls ./*.pdb.gz 2&> /dev/null; then # check if any files are compressed; calling unpigz with an empty arg will cause it to panic
+        unpigz -d ./*.pdb.gz
+    fi
+
+    # construct input file for mtmalign
     ls *.pdb | sed s/\\ /\\n/ > input_list.txt
+
     mtm-align -i input_list.txt -o ${prefix}.pdb
     # -o does not affect the fasta naming, so move it to the new name
     mv ./mTM_result/result.fasta ./mTM_result/${prefix}.aln
 
+    # compress both output files
+    if ${compress}; then
+        pigz -p ${task.cpus} ./mTM_result/${prefix}.aln ./mTM_result/${prefix}.pdb
+    fi
+    tree
+
     # mtm-align -v prints the wrong version 20180725, so extract it from the cosmetic output in the help message
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mTM-align: \$( mtm-align -h | grep -e "\\(Version [[:digit:]]*\\)" | grep -oe "[[:digit:]]*" )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
@@ -41,13 +58,14 @@ process MTMALIGN_ALIGN {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     mkdir mTM_result
-    touch mTM_result/${prefix}.aln
-    touch mTM_result/${prefix}.pdb
+    touch mTM_result/${prefix}.aln${compress ? '.gz' : ''}
+    touch mTM_result/${prefix}.pdb${compress ? '.gz' : ''}
 
     # mtm-align -v prints the wrong version 20180725, so extract it from the cosmetic output in the help message
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mTM-align: \$( mtm-align -h | grep -e "\\(Version [[:digit:]]*\\)" | grep -oe "[[:digit:]]*" )
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/mtmalign/align/meta.yml b/modules/nf-core/mtmalign/align/meta.yml
index 9c4b783649e..1e444e1c6ba 100644
--- a/modules/nf-core/mtmalign/align/meta.yml
+++ b/modules/nf-core/mtmalign/align/meta.yml
@@ -15,6 +15,10 @@ tools:
       tool_dev_url: "http://yanglab.nankai.edu.cn/mTM-align/"
       doi: "10.1093/bioinformatics/btx828"
       licence: ["None"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 input:
   - meta:
       type: map
@@ -23,9 +27,12 @@ input:
         e.g. `[ id:'test']`
   - pdbs:
       type: file
-      description: Input protein structures in PDB format.
+      description: Input protein structures in PDB format. Files may be gzipped or uncompressed.
         They should contain exactly one chain!
       pattern: "*.{pdb}"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
 output:
   - meta:
       type: map
@@ -34,12 +41,12 @@ output:
         e.g. `[ id:'test']`
   - alignment:
       type: file
-      description: Alignment in FASTA format.
-      pattern: "*.aln"
+      description: Alignment in FASTA format. May be gzipped or uncompressed.
+      pattern: "*.aln{.gz,}"
   - structure:
       type: file
-      description: Overlaid structures in PDB format.
-      pattern: "${prefix}.pdb"
+      description: Overlaid structures in PDB format. May be gzipped or uncompressed.
+      pattern: "${prefix}.pdb{.gz,}"
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test b/modules/nf-core/mtmalign/align/tests/main.nf.test
index d3bd9d444f8..cb3f3885b67 100644
--- a/modules/nf-core/mtmalign/align/tests/main.nf.test
+++ b/modules/nf-core/mtmalign/align/tests/main.nf.test
@@ -7,8 +7,9 @@ nextflow_process {
         tag "modules_nfcore"
         tag "mtmalign"
         tag "mtmalign/align"
+        tag "untar"
 
-        test("Should run without failures") {
+        test("Test on seatoxin dataset - uncompressed") {
             setup {
 
                 run("UNTAR") {
@@ -28,6 +29,7 @@ nextflow_process {
                 process {
                     """
                         input[0] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(dir).listFiles().collect()]}
+                        input[1] = false
                     """
                 }
             }
@@ -36,13 +38,53 @@ nextflow_process {
                 assertAll(
                     { assert process.success  },
                     // mTMalign may be nondeterministic, just check if the pdbs are all in there
-                    //assert snapshot(process.out).match()
-                    { assert file(process.out.alignment[0][1]).text.contains(">1.pdb")  },
-                    { assert file(process.out.alignment[0][1]).text.contains(">2.pdb")  },
-                    { assert file(process.out.alignment[0][1]).text.contains(">3.pdb") },
-                    { assert file(process.out.alignment[0][1]).text.contains(">4.pdb") },
-                    { assert file(process.out.alignment[0][1]).text.contains(">5.pdb") },
-                    { assert snapshot(process.out.versions).match("versions") }
+                    //{ assert snapshot(process.out).match() }
+                    { assert path(process.out.alignment[0][1]).getText().contains(">1.pdb") },
+                    { assert path(process.out.alignment[0][1]).getText().contains(">2.pdb") },
+                    { assert path(process.out.alignment[0][1]).getText().contains(">3.pdb") },
+                    { assert path(process.out.alignment[0][1]).getText().contains(">4.pdb") },
+                    { assert path(process.out.alignment[0][1]).getText().contains(">5.pdb") },
+                    { assert snapshot(process.out.versions).match("versions0") }
+                    )
+            }
+        }
+
+        test("Test on seatoxin dataset - compressed") {
+            setup {
+
+                run("UNTAR") {
+                    script "../../../../../modules/nf-core/untar/main.nf"
+                        process {
+                            """
+                                archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                                input[0] = Channel.of(tuple([id:'test'], archive))
+                            """
+                        }
+                }
+            }
+
+            when {
+                params {
+                }
+                process {
+                    """
+                        input[0] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(dir).listFiles().collect()]}
+                        input[1] = true
+                    """
+                }
+            }
+
+            then {
+                assertAll(
+                    { assert process.success  },
+                    // mTMalign may be nondeterministic, just check if the pdbs are all in there
+                    //{ assert snapshot(process.out).match() }
+                    { assert path(process.out.alignment[0][1]).getTextGzip().contains(">1.pdb") },
+                    { assert path(process.out.alignment[0][1]).getTextGzip().contains(">2.pdb") },
+                    { assert path(process.out.alignment[0][1]).getTextGzip().contains(">3.pdb") },
+                    { assert path(process.out.alignment[0][1]).getTextGzip().contains(">4.pdb") },
+                    { assert path(process.out.alignment[0][1]).getTextGzip().contains(">5.pdb") },
+                    { assert snapshot(process.out.versions).match("versions1") }
                     )
             }
         }
diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap
index d9d6c9bed5b..eb321457474 100644
--- a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap
+++ b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap
@@ -1,47 +1,10 @@
 {
-    "Should run without failures": {
+    "versions": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "result.fasta:md5,8400950485c61b741f06c9b936bd2863"
-                    ]
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "result.pdb:md5,53aeaeae0bd1c0c2c887c4215ec44f5e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,4b618e4e98abf72feabb3778d3c39105"
-                ],
-                "alignment": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "result.fasta:md5,8400950485c61b741f06c9b936bd2863"
-                    ]
-                ],
-                "structure": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "result.pdb:md5,53aeaeae0bd1c0c2c887c4215ec44f5e"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,4b618e4e98abf72feabb3778d3c39105"
-                ]
-            }
+            [
+                "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10"
+            ]
         ],
-        "timestamp": "2023-12-04T17:24:24.975306332"
+        "timestamp": "2024-01-25T18:21:22.385207003"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/muscle5/super5/environment.yml b/modules/nf-core/muscle5/super5/environment.yml
index f2c60f16d00..fbaf4a2ef9f 100644
--- a/modules/nf-core/muscle5/super5/environment.yml
+++ b/modules/nf-core/muscle5/super5/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::muscle=5.1
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/muscle5/super5/main.nf b/modules/nf-core/muscle5/super5/main.nf
index 0f58be9461c..87af149b605 100644
--- a/modules/nf-core/muscle5/super5/main.nf
+++ b/modules/nf-core/muscle5/super5/main.nf
@@ -3,15 +3,16 @@ process MUSCLE5_SUPER5 {
     label 'process_medium'
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/muscle:5.1--h9f5acd7_1':
-        'biocontainers/muscle:5.1--h9f5acd7_1' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-8eb01a3c2755c935d070dd03ff2dee698eeb4466:ceb6e65e00346ed20d0d8078dddf9858a7af0fe2-0':
+        'biocontainers/mulled-v2-8eb01a3c2755c935d070dd03ff2dee698eeb4466:ceb6e65e00346ed20d0d8078dddf9858a7af0fe2-0' }"
 
     input:
     tuple val(meta), path(fasta)
+    val(compress)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,16 +21,30 @@ process MUSCLE5_SUPER5 {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     prefix = args.contains('-perm all') ? "${prefix}@" : "${prefix}"
+    def write_output = (compress && !args.contains('-perm all')) ? " -output >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "-output ${prefix}.aln"
+    // muscle internally expands the shell pipe to a file descriptor of the form /dev/fd/<id>
+    // this causes it to fail, unless -output is left at the end of the call
+    // see also clustalo/align
+    // using >() is necessary to preserve the return value,
+    // so nextflow knows to display an error when it failed
     """
     muscle \\
         -super5 ${fasta} \\
-        -output ${prefix}.aln \\
         ${args} \\
-        -threads ${task.cpus}
+        -threads ${task.cpus} \\
+        $write_output
+
+
+    # output may be multiple files if -perm all is set
+    # compress these individually if set to compress output
+    if ${args.contains('-perm all') && compress}; then
+        pigz -p ${task.cpus} *.aln
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         muscle: \$(muscle -version | head -n 1 | cut -d ' ' -f 2 | sed 's/.linux64//')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
@@ -37,11 +52,12 @@ process MUSCLE5_SUPER5 {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln${compress ? '.gz' : ''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         muscle: \$(muscle -version | head -n 1 | cut -d ' ' -f 2 | sed 's/.linux64//')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/muscle5/super5/meta.yml b/modules/nf-core/muscle5/super5/meta.yml
index a789aab0951..057128dc855 100644
--- a/modules/nf-core/muscle5/super5/meta.yml
+++ b/modules/nf-core/muscle5/super5/meta.yml
@@ -11,6 +11,10 @@ tools:
       documentation: "https://drive5.com/muscle5/manual/"
       doi: "10.1101/2021.06.20.449169"
       licence: ["Public Domain"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 input:
   - meta:
       type: map
@@ -21,6 +25,9 @@ input:
       type: file
       description: Input sequences for alignment must be in FASTA format
       pattern: "*.{fasta,fa,fna}"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
 output:
   - meta:
       type: map
@@ -33,11 +40,12 @@ output:
       pattern: "versions.yml"
   - alignment:
       type: file
-      description: Multiple sequence alignment produced in FASTA format
-      pattern: "*.{aln}"
+      description: Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input!
+      pattern: "*.{aln.gz}"
 authors:
   - "@alessiovignoli"
   - "@JoseEspinosa"
 maintainers:
   - "@alessiovignoli"
   - "@JoseEspinosa"
+  - "@lrauschning"
diff --git a/modules/nf-core/muscle5/super5/tests/main.nf.test b/modules/nf-core/muscle5/super5/tests/main.nf.test
index 50821a7f86c..c1541208bcd 100644
--- a/modules/nf-core/muscle5/super5/tests/main.nf.test
+++ b/modules/nf-core/muscle5/super5/tests/main.nf.test
@@ -1,36 +1,72 @@
 nextflow_process {
 
     name "Test Process MUSCLE5_SUPER5"
-    script "../main.nf"
-    process "MUSCLE5_SUPER5"
-    config "./nextflow.config"
+        script "../main.nf"
+        process "MUSCLE5_SUPER5"
+        config "./nextflow.config"
 
-    tag "modules"
-    tag "modules_nfcore"
-    tag "muscle5"
-    tag "muscle5/super5"
+        tag "modules"
+        tag "modules_nfcore"
+        tag "muscle5"
+        tag "muscle5/super5"
 
-    test("sarscov2 - fasta") {
+        test("fasta - align_sequence - uncompressed") {
+            when {
+                process {
+                    """
+                        input[0] = [ [ id:'test' ],
+                        file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                        ]
+                        input[1] = false
+                        """
+                }
+            }
+
+            then {
+                assertAll(
+                        { assert process.success },
+                        { assert snapshot(process.out.alignment).match("alignment - uncompressed")},
+                        )
+            }
+        }
 
-        when {
-            process {
-                """
-                input[0] = [[ id:'test' ],
-                            fasta = [ file(params.test_data['sarscov2']['genome']['proteome_fasta'], checkIfExists: true) ]
-                           ]
-                """
+        test("fasta - align_sequence - compressed") {
+            when {
+                process {
+                    """
+                        input[0] = [ [ id:'test' ],
+                        file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                        ]
+                        input[1] = true
+                        """
+                }
+            }
+
+            then {
+                assertAll(
+                        { assert process.success },
+                        { assert snapshot(process.out.alignment).match("alignment - compressed")},
+                        )
             }
         }
+        test("fasta - align_sequence - compressed - perm_all") {
+            config "./perm_all.config"
+            when {
+                process {
+                    """
+                        input[0] = [ [ id:'test' ],
+                        file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                        ]
+                        input[1] = true
+                        """
+                }
+            }
 
-         then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out.alignment[0][1][0]).match("aln0")},
-                { assert snapshot(process.out.alignment[0][1][1]).match("aln1")},
-                { assert snapshot(process.out.alignment[0][1][2]).match("aln2")},
-                { assert snapshot(process.out.alignment[0][1][3]).match("aln3")},
-                { assert snapshot(process.out.versions).match("versions") }
-            )
+            then {
+                assertAll(
+                        { assert process.success },
+                        { assert snapshot(process.out.alignment).match("perm-all")},
+                        )
+            }
         }
-    }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/muscle5/super5/tests/main.nf.test.snap b/modules/nf-core/muscle5/super5/tests/main.nf.test.snap
index ba665414273..ce7aadf0575 100644
--- a/modules/nf-core/muscle5/super5/tests/main.nf.test.snap
+++ b/modules/nf-core/muscle5/super5/tests/main.nf.test.snap
@@ -1,34 +1,46 @@
 {
-    "aln0": {
+    "alignment - compressed": {
         "content": [
-            "testabc.3.aln:md5,006a173438952c838215cd6cc9b42a3d"
-        ],
-        "timestamp": "2023-11-28T18:01:32.513414439"
-    },
-    "aln2": {
-        "content": [
-            "testbca.3.aln:md5,00496f951481d58bf23bb7690057c59f"
-        ],
-        "timestamp": "2023-11-28T18:01:32.536803426"
-    },
-    "aln1": {
-        "content": [
-            "testacb.3.aln:md5,fc94bb7d0b0308537fa0997c06c5a86f"
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln.gz:md5,46ba556df08f7aabbe5e1ba31d226b6a"
+                ]
+            ]
         ],
-        "timestamp": "2023-11-28T18:01:32.52911204"
+        "timestamp": "2024-02-09T19:08:23.498404397"
     },
-    "versions": {
+    "perm-all": {
         "content": [
             [
-                "versions.yml:md5,eccf3d4f3b7ffc7d1bacb74c4d20304e"
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "testabc.0.aln.gz:md5,46ba556df08f7aabbe5e1ba31d226b6a",
+                        "testacb.0.aln.gz:md5,46ba556df08f7aabbe5e1ba31d226b6a",
+                        "testbca.0.aln.gz:md5,46ba556df08f7aabbe5e1ba31d226b6a",
+                        "testnone.0.aln.gz:md5,46ba556df08f7aabbe5e1ba31d226b6a"
+                    ]
+                ]
             ]
         ],
-        "timestamp": "2023-11-28T17:57:05.227355467"
+        "timestamp": "2024-02-09T19:08:37.386512953"
     },
-    "aln3": {
+    "alignment - uncompressed": {
         "content": [
-            "testnone.3.aln:md5,958666a45eabba897417fc2ade08a21b"
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln:md5,46ba556df08f7aabbe5e1ba31d226b6a"
+                ]
+            ]
         ],
-        "timestamp": "2023-11-28T18:01:32.544996959"
+        "timestamp": "2024-02-09T19:16:25.330353817"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/muscle5/super5/tests/nextflow.config b/modules/nf-core/muscle5/super5/tests/nextflow.config
index f6192f874cd..e69de29bb2d 100644
--- a/modules/nf-core/muscle5/super5/tests/nextflow.config
+++ b/modules/nf-core/muscle5/super5/tests/nextflow.config
@@ -1,3 +0,0 @@
-process {
-    ext.args = '-perturb 3 -perm all'
-}
diff --git a/modules/nf-core/muscle5/super5/tests/perm_all.config b/modules/nf-core/muscle5/super5/tests/perm_all.config
new file mode 100644
index 00000000000..d3502716003
--- /dev/null
+++ b/modules/nf-core/muscle5/super5/tests/perm_all.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = { "-perm all" }
+}
diff --git a/modules/nf-core/tcoffee/align/environment.yml b/modules/nf-core/tcoffee/align/environment.yml
index 6f63405d47e..28f159fd459 100644
--- a/modules/nf-core/tcoffee/align/environment.yml
+++ b/modules/nf-core/tcoffee/align/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::t-coffee=13.46.0.919e8c6b
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
index b09a819fb4d..671aca8eacc 100644
--- a/modules/nf-core/tcoffee/align/main.nf
+++ b/modules/nf-core/tcoffee/align/main.nf
@@ -4,26 +4,30 @@ process TCOFFEE_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/t-coffee:13.46.0.919e8c6b--hfc96bf3_0':
-        'biocontainers/t-coffee:13.46.0.919e8c6b--hfc96bf3_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
+        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
 
     input:
     tuple val(meta) ,  path(fasta)
     tuple val(meta2),  path(tree)
     tuple val(meta3),  path(template), path(accessory_informations)
+    val(compress)
 
     output:
-    tuple val (meta), path ("*.aln"), emit: alignment
-    path "versions.yml" , emit: versions
+    tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def tree_args = tree ? "-usetree $tree" : ""
     def template_args = template ? "-template_file $template" : ""
+    def write_output = compress ? " >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "> ${prefix}.aln"
+    // using >() is necessary to preserve the tcoffee return value,
+    // so nextflow knows to display an error when it failed
     """
     export TEMP='./'
     t_coffee -seq ${fasta} \
@@ -31,23 +35,25 @@ process TCOFFEE_ALIGN {
         $template_args \
         $args \
         -thread ${task.cpus} \
-        -outfile ${prefix}.aln
-
+        -outfile stdout \
+        $write_output
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln${compress ? '.gz':''}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tcoffee/align/meta.yml b/modules/nf-core/tcoffee/align/meta.yml
index 531aa3e4b04..6cfcc72d46a 100644
--- a/modules/nf-core/tcoffee/align/meta.yml
+++ b/modules/nf-core/tcoffee/align/meta.yml
@@ -12,6 +12,10 @@ tools:
       tool_dev_url: "https://github.com/cbcrg/tcoffee"
       doi: "10.1006/jmbi.2000.4042"
       licence: ["GPL v3"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 input:
   - meta:
       type: map
@@ -44,6 +48,9 @@ input:
       type: file
       description: Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures.
       pattern: "*"
+  - compress:
+      type: boolean
+      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
 output:
   - meta:
       type: map
@@ -52,8 +59,8 @@ output:
         e.g. `[ id:'test']`
   - alignment:
       type: file
-      description: Alignment file.
-      pattern: "*.{aln}"
+      description: Alignment file in FASTA format. May be gzipped.
+      pattern: "*.aln{.gz,}"
   - versions:
       type: file
       description: File containing software versions
@@ -64,3 +71,4 @@ authors:
 maintainers:
   - "@luisas"
   - "@JoseEspinosa"
+  - "@lrauschning"
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test
index bb17194c568..9d66f86bf39 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test
@@ -8,6 +8,8 @@ nextflow_process {
     tag "modules_nfcore"
     tag "tcoffee"
     tag "tcoffee/align"
+    tag "famsa/guidetree"
+    tag "untar"
 
     test("fasta - align_sequence") {
 
@@ -21,6 +23,7 @@ nextflow_process {
                            ]
                 input[1] = [[:],[]]
                 input[2] = [[:],[],[]]
+                input[3] = true
                 """
             }
         }
@@ -29,7 +32,33 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.alignment).match("alignment")},
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.versions).match("versions_uncomp") }
+            )
+        }
+    }
+
+    test("fasta - align_sequence - uncompressed") {
+
+        config "./sequence.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = [[:],[],[]]
+                input[3] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.alignment).match("alignment - uncompressed")},
+                { assert snapshot(process.out.versions).match("versions_comp") }
             )
         }
     }
@@ -61,6 +90,7 @@ nextflow_process {
                            ]
                 input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]}
                 input[2] = [ [:], [], [] ]
+                input[3] = true
                 """
             }
         }
@@ -69,7 +99,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out.alignment).match("alignment_guidetree")},
-                { assert snapshot(process.out.versions).match("versions_guidtree") }
+                { assert snapshot(process.out.versions).match("versions_guidetree") }
             )
         }
 
@@ -102,6 +132,7 @@ nextflow_process {
                            ]
                 input[1] = [ [:], [] ]
                 input[2] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], [] ,file(dir).listFiles().collect()]}
+                input[3] = true
                 """
 
             }
@@ -110,10 +141,10 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") },
+                { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") },
                 { assert snapshot(process.out.versions).match("versions_structure") }
             )
         }
 
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
index 79dd44e5707..94b9d4e3cce 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
@@ -2,51 +2,64 @@
     "versions_structure": {
         "content": [
             [
-                "versions.yml:md5,4d38a2c2211ee21b5c1b181e8260f5f7"
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
-        "timestamp": "2023-11-28T12:26:47.937090039"
+        "timestamp": "2024-02-09T19:43:36.590833926"
     },
     "versions": {
         "content": [
             [
-                "versions.yml:md5,4d38a2c2211ee21b5c1b181e8260f5f7"
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
             ]
         ],
-        "timestamp": "2023-11-28T12:26:26.949694794"
+        "timestamp": "2024-02-09T19:42:52.802861054"
     },
-    "versions_guidtree": {
+    "alignment - uncompressed": {
         "content": [
             [
-                "versions.yml:md5,4d38a2c2211ee21b5c1b181e8260f5f7"
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln:md5,bd1db08ad04514cc6d1334598c1a6ef0"
+                ]
             ]
         ],
-        "timestamp": "2023-11-28T12:26:36.766599176"
+        "timestamp": "2024-02-09T19:43:05.936032398"
     },
-    "msa": {
+    "versions_guidetree": {
+        "content": [
+            [
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+            ]
+        ],
+        "timestamp": "2024-02-09T19:43:20.741062719"
+    },
+    "alignment": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln:md5,bd1db08ad04514cc6d1334598c1a6ef0"
+                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
                 ]
             ]
         ],
-        "timestamp": "2023-11-28T12:26:26.904709139"
+        "timestamp": "2024-02-09T19:42:52.774882703"
     },
-    "msa_guidetree": {
+    "alignment_guidetree": {
         "content": [
             [
                 [
                     {
                         "id": "test"
                     },
-                    "test.aln:md5,93bc8adfcd88f7913718eacc13da8e4a"
+                    "test.aln.gz:md5,93bc8adfcd88f7913718eacc13da8e4a"
                 ]
             ]
         ],
-        "timestamp": "2023-11-28T12:26:36.702189365"
+        "timestamp": "2024-02-09T19:43:20.688201033"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/tests/structure.config b/modules/nf-core/tcoffee/align/tests/structure.config
index 4ae9d7acc1a..1cbd9c9c8e1 100644
--- a/modules/nf-core/tcoffee/align/tests/structure.config
+++ b/modules/nf-core/tcoffee/align/tests/structure.config
@@ -1,5 +1,5 @@
 process {
     withName: "TCOFFEE_ALIGN" {
-        ext.args = { "-method TMalign_pair" }
+        ext.args = { "-method TMalign_pair -output fasta_aln" }
     }
 }
diff --git a/modules/nf-core/tcoffee/alncompare/environment.yml b/modules/nf-core/tcoffee/alncompare/environment.yml
index 099528eccf4..dfa14141528 100644
--- a/modules/nf-core/tcoffee/alncompare/environment.yml
+++ b/modules/nf-core/tcoffee/alncompare/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::t-coffee=13.46.0.919e8c6b
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/alncompare/main.nf b/modules/nf-core/tcoffee/alncompare/main.nf
index 75c008af5bb..043158a75ad 100644
--- a/modules/nf-core/tcoffee/alncompare/main.nf
+++ b/modules/nf-core/tcoffee/alncompare/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_ALNCOMPARE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/t-coffee:13.46.0.919e8c6b--hfc96bf3_0':
-        'biocontainers/t-coffee:13.46.0.919e8c6b--hfc96bf3_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
+        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
 
     input:
     tuple val(meta), path(msa), path(ref_msa)
@@ -23,12 +23,14 @@ process TCOFFEE_ALNCOMPARE {
     def metric_name = args.split('compare_mode ')[1].split(' ')[0]
     def header = meta.keySet().join(",")
     def values = meta.values().join(",")
+    def read_msa = msa.getName().endsWith(".gz") ? "<(unpigz -cdf ${msa})" : msa
+    def read_ref = ref_msa.getName().endsWith(".gz") ? "<(unpigz -cdf ${ref_msa})" : ref_msa
 
     """
     export TEMP='./'
     t_coffee -other_pg aln_compare \
-        -al1 ${ref_msa} \
-        -al2 ${msa} \
+        -al1 ${read_ref} \
+        -al2 ${read_msa} \
         ${args} \
         | grep -v "seq1" | grep -v '*' | \
         awk '{ print \$4}' ORS="\t" \
@@ -44,6 +46,7 @@ process TCOFFEE_ALNCOMPARE {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
     stub:
@@ -55,6 +58,7 @@ process TCOFFEE_ALNCOMPARE {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tcoffee/alncompare/meta.yml b/modules/nf-core/tcoffee/alncompare/meta.yml
index 9f85247692b..31502555d9e 100644
--- a/modules/nf-core/tcoffee/alncompare/meta.yml
+++ b/modules/nf-core/tcoffee/alncompare/meta.yml
@@ -12,6 +12,10 @@ tools:
       tool_dev_url: "https://github.com/cbcrg/tcoffee"
       doi: "10.1006/jmbi.2000.4042"
       licence: ["GPL v3"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 
 input:
   - meta:
@@ -21,12 +25,12 @@ input:
         e.g. [ id:'test', ... ]
   - msa:
       type: file
-      description: fasta file containing the alignment to be evaluated
-      pattern: "*.{aln,fa,fasta,fas}"
+      description: fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed
+      pattern: "*.{aln,fa,fasta,fas}{.gz,}"
   - ref_msa:
       type: file
-      description: fasta file containing the reference alignment used for the evaluation
-      pattern: "*.{aln,fa,fasta,fas}"
+      description: fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed
+      pattern: "*.{aln,fa,fasta,fas}{.gz,}"
 
 output:
   - meta:
diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
index 7524515a848..d1fd92e4304 100644
--- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8a30677771f2dc3b61b60702622fdfda"
+                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
                 ],
                 "scores": [
                     [
@@ -22,10 +22,10 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,8a30677771f2dc3b61b60702622fdfda"
+                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
                 ]
             }
         ],
-        "timestamp": "2023-12-13T10:50:50.701336"
+        "timestamp": "2024-01-22T17:08:59.494237269"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/irmsd/environment.yml b/modules/nf-core/tcoffee/irmsd/environment.yml
index 635de77940d..4065fe70bd6 100644
--- a/modules/nf-core/tcoffee/irmsd/environment.yml
+++ b/modules/nf-core/tcoffee/irmsd/environment.yml
@@ -5,3 +5,4 @@ channels:
   - defaults
 dependencies:
   - bioconda::t-coffee=13.46.0.919e8c6b
+  - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/irmsd/main.nf b/modules/nf-core/tcoffee/irmsd/main.nf
index 0c60312ea78..95e6b61efb4 100644
--- a/modules/nf-core/tcoffee/irmsd/main.nf
+++ b/modules/nf-core/tcoffee/irmsd/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_IRMSD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/t-coffee:13.46.0.919e8c6b--hfc96bf3_0':
-        'biocontainers/t-coffee:13.46.0.919e8c6b--hfc96bf3_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
+        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
 
     input:
     tuple  val(meta),  file (msa)
@@ -24,14 +24,19 @@ process TCOFFEE_IRMSD {
     """
     export TEMP='./'
 
+    if [[ \$(basename $msa) == *.gz ]] ; then
+        unpigz -f $msa
+    fi
+
     t_coffee -other_pg irmsd \
-        $msa \
+        \$(basename $msa .gz) \
         $args \
         -template_file $template > ${prefix}.irmsd
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 
@@ -44,6 +49,7 @@ process TCOFFEE_IRMSD {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}')
+        pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' ))
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml
index abee1a3a5d4..f55fca748cf 100644
--- a/modules/nf-core/tcoffee/irmsd/meta.yml
+++ b/modules/nf-core/tcoffee/irmsd/meta.yml
@@ -1,5 +1,5 @@
 name: "tcoffee_irmsd"
-description: Computes irmsd score for a given alignment and the structures.
+description: Computes the irmsd score for a given alignment and the structures.
 keywords:
   - alignment
   - MSA
@@ -12,6 +12,10 @@ tools:
       tool_dev_url: "https://github.com/cbcrg/tcoffee"
       doi: "10.1006/jmbi.2000.4042"
       licence: ["GPL v3"]
+  - "pigz":
+      description: "Parallel implementation of the gzip algorithm."
+      homepage: "https://zlib.net/pigz/"
+      documentation: "https://zlib.net/pigz/pigz.pdf"
 
 input:
   - meta:
@@ -21,11 +25,11 @@ input:
         e.g. [ id:'test', ... ]
   - msa:
       type: file
-      description: fasta file containing the alignment to be evaluated
-      pattern: "*.{aln,fa,fasta,fas}"
+      description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.
+      pattern: "*.{aln,fa,fasta,fas}{.gz,}"
   - template:
       type: file
-      description: Template file matching the structures to the sequences in the alignment
+      description: Template file matching the structures to the sequences in the alignment.
       pattern: "*"
   - structures:
       type: directory
diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
index 1519a66da89..55a574a4616 100644
--- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test
@@ -6,7 +6,9 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "tcoffee"
-    tag "tcoffee/irmsd" 
+    tag "tcoffee/irmsd"
+    tag "untar"
+    tag "pigz/compress"
 
     test("seatoxin") {
 
@@ -24,7 +26,7 @@ nextflow_process {
                 }
             }
         }
-        
+
         when {
             process {
                 """
@@ -35,7 +37,7 @@ nextflow_process {
                 input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
                 """
             }
-            
+
         }
 
         then {
@@ -47,4 +49,51 @@ nextflow_process {
 
     }
 
-}
+    test("seatoxin - compressed") {
+
+        setup {
+
+            run("UNTAR") {
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [ id:'test' ],
+                                 file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                               ]
+
+                    """
+                }
+            }
+
+            run("PIGZ_COMPRESS") {
+                script "../../../pigz/compress/main.nf"
+                process {
+                    """
+                    input[0] = [ [ id:'test' ],
+                                file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                               ]
+
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = PIGZ_COMPRESS.out.archive
+                input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]}
+                """
+            }
+
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.irmsd.get(0).get(1)).getText().contains("1ahl") }
+            )
+        }
+
+    }
+}
\ No newline at end of file