diff --git a/modules/local/create_assembly_metadata_csv/main.nf b/modules/local/create_assembly_metadata_csv/main.nf
index b7d7151..2e8283a 100644
--- a/modules/local/create_assembly_metadata_csv/main.nf
+++ b/modules/local/create_assembly_metadata_csv/main.nf
@@ -12,7 +12,7 @@ process CREATE_ASSEMBLY_METADATA_CSV {
 
     output:
     tuple val(meta), path("${meta.id}_assembly_metadata.csv"), emit: csv
-    path "versions.yml"                                      , emit: versions
+    tuple val("${task.process}"), val('bash'), eval('bash --version | head -n1 | sed "s/.*version //; s/ .*//"'), topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,20 +32,10 @@ process CREATE_ASSEMBLY_METADATA_CSV {
     ${header}
     ${row}
     END_CSV
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
-    END_VERSIONS
     """
 
     stub:
     """
     touch ${meta.id}_assembly_metadata.csv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap b/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap
index bc1aaab..2b37721 100644
--- a/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap
+++ b/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap
@@ -15,7 +15,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                    [
+                        "CREATE_ASSEMBLY_METADATA_CSV",
+                        "bash",
+                        "5.2.37(1)-release"
+                    ]
                 ],
                 "csv": [
                     [
@@ -28,17 +32,14 @@
                         },
                         "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
                 ]
             }
         ],
+        "timestamp": "2026-07-07T13:48:39.201846",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "25.04.1"
-        },
-        "timestamp": "2026-04-27T14:51:27.130061"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test_create_assembly_metadata_csv - stub": {
         "content": [
@@ -56,7 +57,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
+                    [
+                        "CREATE_ASSEMBLY_METADATA_CSV",
+                        "bash",
+                        "5.2.37(1)-release"
+                    ]
                 ],
                 "csv": [
                     [
@@ -69,16 +74,13 @@
                         },
                         "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
                 ]
             }
         ],
+        "timestamp": "2026-07-07T13:48:46.340926",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "25.04.1"
-        },
-        "timestamp": "2026-04-27T14:51:32.249848"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/local/create_genome_metadata_tsv/main.nf b/modules/local/create_genome_metadata_tsv/main.nf
index d451f11..e78a7af 100644
--- a/modules/local/create_genome_metadata_tsv/main.nf
+++ b/modules/local/create_genome_metadata_tsv/main.nf
@@ -12,7 +12,7 @@ process CREATE_GENOME_METADATA_TSV {
 
     output:
     tuple val(meta), path("${meta.id}_genome_metadata.tsv"), emit: tsv
-    path "versions.yml"                                    , emit: versions
+    tuple val("${task.process}"), val('bash'), eval('bash --version | head -n1 | sed "s/.*version //; s/ .*//"'), topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -63,20 +63,10 @@ process CREATE_GENOME_METADATA_TSV {
     ${header}
     ${row}
     END_TSV
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
-    END_VERSIONS
     """
 
     stub:
     """
     touch ${meta.id}_genome_metadata.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap b/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap
index 395a4e9..a073053 100644
--- a/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap
+++ b/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap
@@ -26,7 +26,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
+                    [
+                        "CREATE_GENOME_METADATA_TSV",
+                        "bash",
+                        "5.2.37(1)-release"
+                    ]
                 ],
                 "tsv": [
                     [
@@ -50,17 +54,14 @@
                         },
                         "test_genome_genome_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
                 ]
             }
         ],
+        "timestamp": "2026-07-07T13:49:45.599115",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "25.04.1"
-        },
-        "timestamp": "2026-04-27T14:54:46.395718"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test_create_genome_metadata_tsv": {
         "content": [
@@ -89,7 +90,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
+                    [
+                        "CREATE_GENOME_METADATA_TSV",
+                        "bash",
+                        "5.2.37(1)-release"
+                    ]
                 ],
                 "tsv": [
                     [
@@ -113,16 +118,13 @@
                         },
                         "test_genome_genome_metadata.tsv:md5,64562a85d19fe5893cad0e89e894058a"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
                 ]
             }
         ],
+        "timestamp": "2026-07-07T13:49:37.674712",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "25.04.1"
-        },
-        "timestamp": "2026-04-27T14:54:41.692391"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1f628b6..59c6dc0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/master/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/main/nextflow_schema.json",
     "title": "nf-core/seqsubmit pipeline parameters",
     "description": "Submit sequences, assemblies, MAGs, etc., to public archives",
     "type": "object",
@@ -17,7 +17,7 @@
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|tsv|yaml|yml|json)$",
                     "description": "Path to comma-separated file describing the data to be submitted. Format depends on the pipeline mode (mags/bins/metagenomic_assemblies/reads).",
                     "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a set of columns depending on the type of data being submitted. See [usage docs](https://nf-co.re/seqsubmit/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
diff --git a/workflows/assemblysubmit.nf b/workflows/assemblysubmit.nf
index 2acf2b1..84a9dc8 100644
--- a/workflows/assemblysubmit.nf
+++ b/workflows/assemblysubmit.nf
@@ -139,7 +139,6 @@ workflow ASSEMBLYSUBMIT {
     CREATE_ASSEMBLY_METADATA_CSV(
         assemblies_with_coverage
     )
-    ch_versions = ch_versions.mix(CREATE_ASSEMBLY_METADATA_CSV.out.versions)
 
     // Concatenate assembly metadata CSVs into single file to publish
     CONCAT_METADATA (
diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf
index 18edd96..8c1df8e 100644
--- a/workflows/genomesubmit.nf
+++ b/workflows/genomesubmit.nf
@@ -252,7 +252,6 @@ workflow GENOMESUBMIT {
     CREATE_GENOME_METADATA_TSV (
         fasta_updated_with_taxonomy
     )
-    ch_versions = ch_versions.mix(CREATE_GENOME_METADATA_TSV.out.versions)
 
     // Collect all TSV rows into a single file
     CONCAT_METADATA (