diff --git a/config/annotation_preprocessing_modules.config b/config/annotation_preprocessing_modules.config
index b73fd81..3c202dc 100644
--- a/config/annotation_preprocessing_modules.config
+++ b/config/annotation_preprocessing_modules.config
@@ -19,7 +19,7 @@ process {
     withName: 'BUSCO' {
         time       = 2.d
         tag        = { "$lineage:$meta.id" }
-        ext.args   = '--mode genome --tar'
+        ext.args   = '--tar'
         publishDir = [
             path: "${params.outdir}/${publish_subdir}/busco", 
             mode: params.publishDir_mode,
diff --git a/modules.json b/modules.json
index bd029df..0691969 100644
--- a/modules.json
+++ b/modules.json
@@ -12,7 +12,7 @@
           },
           "busco": {
             "branch": "master",
-            "git_sha": "6d6552cb582f56b6101c452e16ee7c23073f91de",
+            "git_sha": "e3126f437c336c826f242842fe51769cfce0ec2d",
             "installed_by": ["modules"]
           },
           "fastp": {
diff --git a/modules/nf-core/busco/environment.yml b/modules/nf-core/busco/environment.yml
new file mode 100644
index 0000000..f872d05
--- /dev/null
+++ b/modules/nf-core/busco/environment.yml
@@ -0,0 +1,7 @@
+name: busco
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::busco=5.5.0
diff --git a/modules/nf-core/busco/main.nf b/modules/nf-core/busco/main.nf
index 95586b0..e710040 100644
--- a/modules/nf-core/busco/main.nf
+++ b/modules/nf-core/busco/main.nf
@@ -2,13 +2,14 @@ process BUSCO {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::busco=5.4.3"
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/busco:5.4.3--pyhdfd78af_0':
-        'biocontainers/busco:5.4.3--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/busco:5.5.0--pyhdfd78af_0':
+        'biocontainers/busco:5.5.0--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path('tmp_input/*')
+    val mode                              // Required:    One of genome, proteins, or transcriptome
     val lineage                           // Required:    lineage to check against, "auto" enables --auto-lineage instead
     path busco_lineages_path              // Recommended: path to busco lineages - downloads if not set
     path config_file                      // Optional:    busco configuration file
@@ -29,11 +30,14 @@ process BUSCO {
     task.ext.when == null || task.ext.when
 
     script:
+    if ( mode !in [ 'genome', 'proteins', 'transcriptome' ] ) {
+        error "Mode must be one of 'genome', 'proteins', or 'transcriptome'."
+    }
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}-${lineage}"
     def busco_config = config_file ? "--config $config_file" : ''
     def busco_lineage = lineage.equals('auto') ? '--auto-lineage' : "--lineage_dataset ${lineage}"
-    def busco_lineage_dir = busco_lineages_path ? "--offline --download_path ${busco_lineages_path}" : ''
+    def busco_lineage_dir = busco_lineages_path ? "--download_path ${busco_lineages_path}" : ''
     """
     # Nextflow changes the container --entrypoint to /bin/bash (container default entrypoint: /usr/local/env-execute)
     # Check for container variable initialisation script and source it.
@@ -69,6 +73,7 @@ process BUSCO {
         --cpu $task.cpus \\
         --in "\$INPUT_SEQS" \\
         --out ${prefix}-busco \\
+        --mode $mode \\
         $busco_lineage \\
         $busco_lineage_dir \\
         $busco_config \\
diff --git a/modules/nf-core/busco/meta.yml b/modules/nf-core/busco/meta.yml
index 77d15fb..90b30d4 100644
--- a/modules/nf-core/busco/meta.yml
+++ b/modules/nf-core/busco/meta.yml
@@ -13,7 +13,6 @@ tools:
       tool_dev_url: https://gitlab.com/ezlab/busco
       doi: "10.1007/978-1-4939-9173-0_14"
       licence: ["MIT"]
-
 input:
   - meta:
       type: map
@@ -24,6 +23,10 @@ input:
       type: file
       description: Nucleic or amino acid sequence file in FASTA format.
       pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}"
+  - mode:
+      type: string
+      description: The mode to run Busco in. One of genome, proteins, or transcriptome
+      pattern: "{genome,proteins,transcriptome}"
   - lineage:
       type: string
       description: The BUSCO lineage to use, or "auto" to automatically select lineage
@@ -33,7 +36,6 @@ input:
   - config_file:
       type: file
       description: Path to BUSCO config file.
-
 output:
   - meta:
       type: map
@@ -80,10 +82,15 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-
 authors:
   - "@priyanka-surana"
   - "@charles-plessy"
   - "@mahesh-panchal"
   - "@muffato"
   - "@jvhagey"
+maintainers:
+  - "@priyanka-surana"
+  - "@charles-plessy"
+  - "@mahesh-panchal"
+  - "@muffato"
+  - "@jvhagey"
diff --git a/subworkflows/annotation_preprocessing/main.nf b/subworkflows/annotation_preprocessing/main.nf
index 25b4242..d85c240 100644
--- a/subworkflows/annotation_preprocessing/main.nf
+++ b/subworkflows/annotation_preprocessing/main.nf
@@ -17,13 +17,17 @@ workflow ANNOTATION_PREPROCESSING {
     
     ASSEMBLY_PURIFY( genome_assembly )
     ASSEMBLY_STATS( genome_assembly.mix( ASSEMBLY_PURIFY.out.fasta ) )
-    BUSCO( 
-        ASSEMBLY_PURIFY.out.fasta
-            .combine( ch_busco_lineage )
-            .multiMap { fasta, lineage ->
-                ch_fasta: [ [ id: fasta.baseName ], fasta ]
-                ch_busco: lineage
-            },
+
+    ch_busco_in = ASSEMBLY_PURIFY.out.fasta
+        .combine( ch_busco_lineage )
+        .multiMap { fasta, lineage ->
+            fasta: [ [ id: fasta.baseName ], fasta ]
+            lineage: lineage
+        }
+    BUSCO (
+        ch_busco_in.fasta,
+        "genome",
+        ch_busco_in.lineage,
         params.busco_lineages_path ? file( params.busco_lineages_path, checkIfExists: true ) : [],
         []
     )