diff --git a/modules/nf-core/tcoffee/align/environment.yml b/modules/nf-core/tcoffee/align/environment.yml
index 9ea79e25aa0..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/align/environment.yml
+++ b/modules/nf-core/tcoffee/align/environment.yml
@@ -4,6 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
-  - bioconda::tmalign=20170708
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
index aae80839658..80c525a7965 100644
--- a/modules/nf-core/tcoffee/align/main.nf
+++ b/modules/nf-core/tcoffee/align/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'oras://community.wave.seqera.io/library/t-coffee_tmalign_pigz:f861f2f8f266c2fe':
-        'community.wave.seqera.io/library/t-coffee_tmalign_pigz:be7dac2ae6aba380' }"
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple val(meta) ,  path(fasta)
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 65d93688d02..48c74ff04c2 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
@@ -2,62 +2,62 @@
     "align_sequence - uncompressed - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T10:38:34.006567221"
+        "timestamp": "2025-02-19T08:01:20.749130634"
     },
     "align_with_structure - uncompressed - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:36:55.402470994"
+        "timestamp": "2025-02-19T08:01:53.240805233"
     },
     "align_sequence - compressed - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T10:38:18.99603304"
+        "timestamp": "2025-02-19T08:01:05.500957902"
     },
     "align_with_guide_tree - uncompressed - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T10:38:48.044669392"
+        "timestamp": "2025-02-19T08:01:36.781063137"
     },
     "align_with_lib - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T10:47:34.909457138"
+        "timestamp": "2025-02-19T08:02:04.884176473"
     },
     "align_sequence - uncompressed - seatoxin - stub": {
         "content": [
@@ -74,7 +74,7 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                    "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
                 ],
                 "alignment": [
                     [
@@ -88,14 +88,14 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+                    "versions.yml:md5,95c81894b17f1e7cd917df513c27458e"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:37:06.112822121"
+        "timestamp": "2025-02-19T08:02:17.843814218"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/alncompare/environment.yml b/modules/nf-core/tcoffee/alncompare/environment.yml
index c17fbb8f14e..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/alncompare/environment.yml
+++ b/modules/nf-core/tcoffee/alncompare/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/alncompare/main.nf b/modules/nf-core/tcoffee/alncompare/main.nf
index e4f46866282..2c9778c1d5d 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/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
-        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple val(meta), path(msa), path(ref_msa)
@@ -33,6 +33,8 @@ process TCOFFEE_ALNCOMPARE {
     fi
 
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
     t_coffee -other_pg aln_compare \
         -al1 ${ref_msa} \
         -al2 uncompressed_msa.fa \
@@ -60,6 +62,8 @@ process TCOFFEE_ALNCOMPARE {
     """
     # Otherwise, tcoffee will crash when calling its version
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
     touch "${prefix}.scores"
 
     cat <<-END_VERSIONS > versions.yml
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 90e97dd5dbe..0ca83dcda9b 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:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ],
                 "scores": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-11-26T08:54:31.823528877"
+        "timestamp": "2025-02-19T08:10:13.98747038"
     },
     "seatoxin - stub": {
         "content": [
@@ -44,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ],
                 "scores": [
                     [
@@ -55,15 +55,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T09:48:00.328461809"
+        "timestamp": "2025-02-19T08:10:31.783898713"
     },
     "seatoxin": {
         "content": [
@@ -77,7 +77,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ],
                 "scores": [
                     [
@@ -88,14 +88,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d"
+                    "versions.yml:md5,bf6ee077f62052ec8e3ee8d836f50c87"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-01-22T17:08:59.494237269"
+        "timestamp": "2025-02-19T08:10:01.028826144"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/consensus/environment.yml b/modules/nf-core/tcoffee/consensus/environment.yml
index c17fbb8f14e..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/consensus/environment.yml
+++ b/modules/nf-core/tcoffee/consensus/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/consensus/main.nf b/modules/nf-core/tcoffee/consensus/main.nf
index d0567b8d01b..f2de15fad1a 100644
--- a/modules/nf-core/tcoffee/consensus/main.nf
+++ b/modules/nf-core/tcoffee/consensus/main.nf
@@ -4,9 +4,8 @@ process TCOFFEE_CONSENSUS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/5e/5e5c1c07cc0099dacea172348bc78f9a9baab592ce3ece89873703b9e963d269/data':
-        'community.wave.seqera.io/library/t-coffee_pigz:c98a6c87c62d9df6' }"
-
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple val(meta) , path(aln)
@@ -29,6 +28,9 @@ process TCOFFEE_CONSENSUS {
     def write_output = compress ? " | pigz -cp ${task.cpus} > ${prefix}.aln.gz" : ""
     """
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     t_coffee -aln ${aln} \
         $tree_args \
         $args \
@@ -47,6 +49,8 @@ process TCOFFEE_CONSENSUS {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
     touch ${prefix}.aln${compress ? '.gz':''}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
index 4af4326217f..5393ab2558a 100644
--- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap
@@ -2,11 +2,15 @@
     "consensus - no tree - uncompressed - seatoxin ": {
         "content": [
             [
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26",
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26"
             ]
         ],
-        "timestamp": "2024-09-18T13:54:43.924522245"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:13:46.582982023"
     },
     "consensus - stub": {
         "content": [
@@ -29,8 +33,8 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
-                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
+                    "versions.yml:md5,96aeed9939a911a37421af7e88431a26",
+                    "versions.yml:md5,96aeed9939a911a37421af7e88431a26"
                 ],
                 "alignment": [
                     [
@@ -50,29 +54,41 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
-                    "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
+                    "versions.yml:md5,96aeed9939a911a37421af7e88431a26",
+                    "versions.yml:md5,96aeed9939a911a37421af7e88431a26"
                 ]
             }
         ],
-        "timestamp": "2024-10-18T11:41:11.216683"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:14:44.325890293"
     },
     "consensus - tree - compressed- seatoxin": {
         "content": [
             [
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26",
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26"
             ]
         ],
-        "timestamp": "2024-09-18T13:55:03.627733582"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:14:24.230709196"
     },
     "consensus_evaluation - no tree - uncompressed - seatoxin ": {
         "content": [
             [
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1",
-                "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1"
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26",
+                "versions.yml:md5,96aeed9939a911a37421af7e88431a26"
             ]
         ],
-        "timestamp": "2024-10-18T11:43:51.839734"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:14:05.703271958"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/extractfrompdb/environment.yml b/modules/nf-core/tcoffee/extractfrompdb/environment.yml
index 9feadcf3c08..07b8a9e73a1 100644
--- a/modules/nf-core/tcoffee/extractfrompdb/environment.yml
+++ b/modules/nf-core/tcoffee/extractfrompdb/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
diff --git a/modules/nf-core/tcoffee/extractfrompdb/main.nf b/modules/nf-core/tcoffee/extractfrompdb/main.nf
index 70b14bd958b..e04415148fe 100644
--- a/modules/nf-core/tcoffee/extractfrompdb/main.nf
+++ b/modules/nf-core/tcoffee/extractfrompdb/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_EXTRACTFROMPDB {
 
     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' }"
+        'oras://community.wave.seqera.io/library/t-coffee:13.46.1.b8b01e06--b0a9122109906f7c':
+        'community.wave.seqera.io/library/t-coffee:13.46.1.b8b01e06--6dba321d206c56ab' }"
 
     input:
     tuple val(meta), path(pdb)
@@ -23,6 +23,9 @@ process TCOFFEE_EXTRACTFROMPDB {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     t_coffee -other_pg extract_from_pdb \
         -infile ${pdb} \
         $args \
@@ -40,6 +43,9 @@ process TCOFFEE_EXTRACTFROMPDB {
     """
     # Otherwise, tcoffee will crash when calling its version
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     touch "${prefix}.pdb"
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/extractfrompdb/tests/main.nf.test.snap b/modules/nf-core/tcoffee/extractfrompdb/tests/main.nf.test.snap
index 28406eba4d5..b7ffa9258fa 100644
--- a/modules/nf-core/tcoffee/extractfrompdb/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/extractfrompdb/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3ee943561db268aeeb8ebae110debd83"
+                    "versions.yml:md5,a6b262900f5749525990c4a1dbd3ec3a"
                 ],
                 "formatted_pdb": [
                     [
@@ -22,15 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3ee943561db268aeeb8ebae110debd83"
+                    "versions.yml:md5,a6b262900f5749525990c4a1dbd3ec3a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:45:38.462425167"
+        "timestamp": "2025-02-19T09:05:55.935531255"
     },
     "seatoxin": {
         "content": [
@@ -40,29 +40,29 @@
                         {
                             "id": "test"
                         },
-                        "test.pdb:md5,d71e4feec5e11e98f9e3beb1f3ba0085"
+                        "test.pdb:md5,f4d68827f3a77d8439a6f82036a0bda2"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,3ee943561db268aeeb8ebae110debd83"
+                    "versions.yml:md5,a6b262900f5749525990c4a1dbd3ec3a"
                 ],
                 "formatted_pdb": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.pdb:md5,d71e4feec5e11e98f9e3beb1f3ba0085"
+                        "test.pdb:md5,f4d68827f3a77d8439a6f82036a0bda2"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,3ee943561db268aeeb8ebae110debd83"
+                    "versions.yml:md5,a6b262900f5749525990c4a1dbd3ec3a"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:45:33.28185662"
+        "timestamp": "2025-02-19T09:05:33.92596781"
     }
 }
\ 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 c17fbb8f14e..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/irmsd/environment.yml
+++ b/modules/nf-core/tcoffee/irmsd/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/irmsd/main.nf b/modules/nf-core/tcoffee/irmsd/main.nf
index be6b6a11bc5..ef76c15ca86 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/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
-        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple  val(meta),  path (msa)
@@ -23,7 +23,8 @@ process TCOFFEE_IRMSD {
     prefix = task.ext.prefix ?: "${msa.baseName}"
     """
     export TEMP='./'
-
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
     if [[ \$(basename $msa) == *.gz ]] ; then
         unpigz -f $msa
     fi
@@ -46,6 +47,8 @@ process TCOFFEE_IRMSD {
     """
     # Otherwise, tcoffee will crash when calling its version
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
     touch ${prefix}.irmsd
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
index f7d835b7cf8..88c863861b7 100644
--- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap
@@ -2,26 +2,26 @@
     "seatoxin - compressed": {
         "content": [
             [
-                "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
+                "versions.yml:md5,37a65eeb2bbaf4430226c13e887455b5"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:40:19.044094915"
+        "timestamp": "2025-02-19T08:40:55.045504615"
     },
     "seatoxin": {
         "content": [
             [
-                "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
+                "versions.yml:md5,37a65eeb2bbaf4430226c13e887455b5"
             ]
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-12-17T19:40:09.998024561"
+        "timestamp": "2025-02-19T08:40:28.430368371"
     },
     "seatoxin - uncompressed - stub": {
         "content": [
@@ -35,7 +35,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
+                    "versions.yml:md5,37a65eeb2bbaf4430226c13e887455b5"
                 ],
                 "irmsd": [
                     [
@@ -46,14 +46,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6"
+                    "versions.yml:md5,37a65eeb2bbaf4430226c13e887455b5"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T10:15:36.874290895"
+        "timestamp": "2025-02-19T08:41:16.70093499"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/regressive/environment.yml b/modules/nf-core/tcoffee/regressive/environment.yml
index c17fbb8f14e..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/regressive/environment.yml
+++ b/modules/nf-core/tcoffee/regressive/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap b/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap
index 2445b0986d5..d686df37db1 100644
--- a/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap
@@ -5,7 +5,11 @@
                 "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af"
             ]
         ],
-        "timestamp": "2024-10-18T11:10:07.232451"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:28:00.231756882"
     },
     "align_sequence - compressed - seatoxin": {
         "content": [
@@ -13,7 +17,11 @@
                 "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af"
             ]
         ],
-        "timestamp": "2024-10-18T11:32:03.211575"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:27:46.158183014"
     },
     "align_with_guide_tree - uncompressed - seatoxin": {
         "content": [
@@ -21,7 +29,11 @@
                 "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af"
             ]
         ],
-        "timestamp": "2024-10-18T11:32:23.841131"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:28:13.545161936"
     },
     "align_sequence - uncompressed - seatoxin - stub": {
         "content": [
@@ -37,6 +49,10 @@
                 "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af"
             ]
         ],
-        "timestamp": "2024-10-18T11:10:21.369064"
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-02-19T09:28:30.733443807"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/seqreformat/environment.yml b/modules/nf-core/tcoffee/seqreformat/environment.yml
index 9feadcf3c08..07b8a9e73a1 100644
--- a/modules/nf-core/tcoffee/seqreformat/environment.yml
+++ b/modules/nf-core/tcoffee/seqreformat/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf b/modules/nf-core/tcoffee/seqreformat/main.nf
index 04617b01ffd..c6ea48fd5dd 100644
--- a/modules/nf-core/tcoffee/seqreformat/main.nf
+++ b/modules/nf-core/tcoffee/seqreformat/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_SEQREFORMAT {
 
     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' }"
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple val(meta), path(infile)
@@ -23,6 +23,9 @@ process TCOFFEE_SEQREFORMAT {
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     t_coffee -other_pg seq_reformat \
         -in ${infile} \
         $args \
@@ -40,6 +43,9 @@ process TCOFFEE_SEQREFORMAT {
     """
     # Otherwise, tcoffee will crash when calling its version
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     touch "${prefix}.txt"
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
index 185f24d8f55..a58303d53a0 100644
--- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap
@@ -10,14 +10,14 @@
                 ]
             ],
             [
-                "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
+                "versions.yml:md5,a9310e6837f0e4ddf6a5a6e8b465351f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T09:53:55.165479364"
+        "timestamp": "2025-02-19T08:52:48.068857066"
     },
     "seatoxin": {
         "content": [
@@ -30,13 +30,13 @@
                 ]
             ],
             [
-                "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14"
+                "versions.yml:md5,a9310e6837f0e4ddf6a5a6e8b465351f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T09:53:33.814075197"
+        "timestamp": "2025-02-19T08:52:29.963402675"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml
index c17fbb8f14e..bbd810df64a 100644
--- a/modules/nf-core/tcoffee/tcs/environment.yml
+++ b/modules/nf-core/tcoffee/tcs/environment.yml
@@ -4,5 +4,5 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::t-coffee=13.46.0.919e8c6b
+  - bioconda::t-coffee=13.46.1.b8b01e06
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/tcoffee/tcs/main.nf b/modules/nf-core/tcoffee/tcs/main.nf
index 9080a317479..97329f5dca8 100644
--- a/modules/nf-core/tcoffee/tcs/main.nf
+++ b/modules/nf-core/tcoffee/tcs/main.nf
@@ -4,8 +4,8 @@ process TCOFFEE_TCS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0':
-        'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }"
+        'oras://community.wave.seqera.io/library/t-coffee_pigz:91ac7e26b23bb246':
+        'community.wave.seqera.io/library/t-coffee_pigz:7d1373a24f76afe6' }"
 
     input:
     tuple val(meta) , path(msa)
@@ -28,6 +28,9 @@ process TCOFFEE_TCS {
     def unzipped_name = msa.toString() - '.gz'
     """
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     filename=${msa}
     if [[ \$(basename $msa) == *.gz ]] ; then
         unpigz -f $msa
@@ -65,6 +68,9 @@ process TCOFFEE_TCS {
     """
     # Otherwise, tcoffee will crash when calling its version
     export TEMP='./'
+    export TMP_4_TCOFFEE="./"
+    export HOME="./"
+
     touch ${prefix}.tcs
     touch ${prefix}.scores
 
diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
index 80da751875b..9f010dd85b2 100644
--- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap
@@ -2,14 +2,14 @@
     "tcs - seatoxin - compressed": {
         "content": [
             [
-                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+                "versions.yml:md5,696cea7c0ca72bf5aae47d05df2276d8"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T13:13:16.017532678"
+        "timestamp": "2025-02-19T08:02:50.049720694"
     },
     "tcs - seatoxin - stub": {
         "content": [
@@ -31,7 +31,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+                    "versions.yml:md5,696cea7c0ca72bf5aae47d05df2276d8"
                 ],
                 "scores": [
                     [
@@ -50,38 +50,38 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+                    "versions.yml:md5,696cea7c0ca72bf5aae47d05df2276d8"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T09:59:35.62776554"
+        "timestamp": "2025-02-19T08:03:13.55612748"
     },
     "tcs - seatoxin - lib": {
         "content": [
             [
-                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+                "versions.yml:md5,696cea7c0ca72bf5aae47d05df2276d8"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T13:13:32.306127259"
+        "timestamp": "2025-02-19T08:03:03.442861443"
     },
     "tcs - seatoxin": {
         "content": [
             [
-                "versions.yml:md5,99775735c64e1ae150252a3b09576e91"
+                "versions.yml:md5,696cea7c0ca72bf5aae47d05df2276d8"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
         },
-        "timestamp": "2024-09-16T13:13:00.253922777"
+        "timestamp": "2025-02-19T08:02:34.071353672"
     }
 }
\ No newline at end of file