diff --git a/modules/local/crispresso2/functions.nf b/modules/local/crispresso2/functions.nf
deleted file mode 100644
index da9da09..0000000
--- a/modules/local/crispresso2/functions.nf
+++ /dev/null
@@ -1,68 +0,0 @@
-//
-//  Utility functions used in nf-core DSL2 module files
-//
-
-//
-// Extract name of software tool from process name using $task.process
-//
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-//
-// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
-//
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args            = args.args ?: ''
-    options.args2           = args.args2 ?: ''
-    options.args3           = args.args3 ?: ''
-    options.publish_by_meta = args.publish_by_meta ?: []
-    options.publish_dir     = args.publish_dir ?: ''
-    options.publish_files   = args.publish_files
-    options.suffix          = args.suffix ?: ''
-    return options
-}
-
-//
-// Tidy up and join elements of a list to return a path string
-//
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
-    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-//
-// Function to save/publish module results
-//
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions  = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_meta) {
-            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
-            for (key in key_list) {
-                if (args.meta && key instanceof String) {
-                    def path = key
-                    if (args.meta.containsKey(key)) {
-                        path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
-                    }
-                    path = path instanceof String ? path : ''
-                    path_list.add(path)
-                }
-            }
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}
diff --git a/modules/local/crispresso2/main.nf b/modules/local/crispresso2/main.nf
deleted file mode 100644
index 17b0886..0000000
--- a/modules/local/crispresso2/main.nf
+++ /dev/null
@@ -1,41 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-options        = initOptions(params.options)
-
-process CRISPRESSO2 {
-    tag "$meta.id"
-    label 'process_medium'
-    publishDir "${params.outdir}",
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::crispresso2=2.1.2" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/crispresso2:2.1.2--py27heb79e2c_0"
-    } else {
-        container "quay.io/biocontainers/crispresso2:2.1.2--py27heb79e2c_0"
-    }
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("*.merged.*.fastq.gz"), emit: reads
-    path "*.hist"                            , emit: hist
-    path "*.version.txt"                      , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
-    def merged   = "-o ${prefix}.merged"
-    def input_reads = "${reads[0]} ${reads[1]}"
-    """
-    flash2 \\
-        $options.args \\
-        $merged \\
-        -z \\
-        $input_reads
-    echo \$(flash2 --version) > ${software}.version.txt
-    """
-}
diff --git a/modules/local/crispresso2/meta.yml b/modules/local/crispresso2/meta.yml
deleted file mode 100644
index 9cf242e..0000000
--- a/modules/local/crispresso2/meta.yml
+++ /dev/null
@@ -1,49 +0,0 @@
-name: flash2
-description: Perform merging of mate paired-end sequencing reads
-keywords:
-  - sort
-  - reads merging
-  - merge mate pairs
-tools:
-  - flash2:
-      description: |
-        Merge mates from fragments that are shorter than twice the read length
-      homepage: https://github.com/dstreett/FLASH2
-      documentation: {}
-      doi: 10.1093/bioinformatics/btr507
-      licence: ['GPL v3+']
-
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: |
-        List of input FastQ files of size 2; i.e., paired-end data.
-      pattern: "*fastq.gz"
-
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: The merged fastq reads
-      pattern: "*fastq.gz"
-  - histogram:
-      type: file
-      description: Numeric histogram of merged read lengths
-      pattern: "*.hist"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "*.{version.txt}"
-
-authors:
-  - "@Erkison"
-  - "@vaofford"
diff --git a/modules/local/cutadapt/main.nf b/modules/local/cutadapt/main.nf
index 0afe801..1c7bda9 100644
--- a/modules/local/cutadapt/main.nf
+++ b/modules/local/cutadapt/main.nf
@@ -12,11 +12,8 @@ process CUTADAPT {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? 'bioconda::cutadapt=4.4' : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/cutadapt:4.4--py39hf95cd2a_1'
-    } else {
-        container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
-    }
+    container 'quay.io/biocontainers/cutadapt:4.4--py39hf95cd2a_1'
+    
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/flash2/main.nf b/modules/local/flash2/main.nf
index 815d9f0..03e074f 100644
--- a/modules/local/flash2/main.nf
+++ b/modules/local/flash2/main.nf
@@ -11,11 +11,7 @@ process FLASH2 {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::flash=2.2.00" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/pyquest/main.nf b/modules/local/pyquest/main.nf
index bbb78c8..c468fa5 100644
--- a/modules/local/pyquest/main.nf
+++ b/modules/local/pyquest/main.nf
@@ -12,11 +12,7 @@ process PYQUEST {
 
     // Keep for when container is public
     /*
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/flash2:2.2.00--h5bf99c6_3"
-    } else {
-        container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
-    }
+    container "quay.io/biocontainers/flash2:2.2.00--h5bf99c6_3"
     */
     container "quay.io/wtsicgp/pyquest:1.1.0"
 
diff --git a/modules/local/pyquest_library_converter/main.nf b/modules/local/pyquest_library_converter/main.nf
index 293f98c..0f0889c 100644
--- a/modules/local/pyquest_library_converter/main.nf
+++ b/modules/local/pyquest_library_converter/main.nf
@@ -10,12 +10,8 @@ process TRANSFORM_LIBRARY_FOR_PYQUEST {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pyquest', meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? null : null)
 
-    conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/python:3.8.3"
-    } else {
-        container "quay.io/biocontainers/python:3.8.3"
-    }
+    conda (params.enable_conda ? "conda-forge::python=3.12.7" : null)
+    container "docker.io/python:3.12.7-alpine3.20"
 
     input:
         path(oligo_library)
diff --git a/modules/local/samtools/bam2fq/main.nf b/modules/local/samtools/bam2fq/main.nf
index 80495b1..51380da 100644
--- a/modules/local/samtools/bam2fq/main.nf
+++ b/modules/local/samtools/bam2fq/main.nf
@@ -3,9 +3,7 @@ process SAMTOOLS_BAM2FQ {
     label 'process_low'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/samtools:1.15--h1170115_1' :
-        'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
+    container 'quay.io/biocontainers/samtools:1.15--h1170115_1'
 
     input:
     tuple val(meta), path(inputbam)
diff --git a/modules/local/seqkit_seq/main.nf b/modules/local/seqkit_seq/main.nf
index 5e62142..9616e26 100644
--- a/modules/local/seqkit_seq/main.nf
+++ b/modules/local/seqkit_seq/main.nf
@@ -13,12 +13,7 @@ process SEQKIT_SEQ {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_seq', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)
diff --git a/modules/local/seqkit_stats/main.nf b/modules/local/seqkit_stats/main.nf
index f6423ea..8b2ef1f 100644
--- a/modules/local/seqkit_stats/main.nf
+++ b/modules/local/seqkit_stats/main.nf
@@ -13,12 +13,7 @@ process SEQKIT_STATS {
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)+'_stats', meta:meta, publish_by_meta:['id']) }
 
     conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
-
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
-    } else {
-        container "quay.io/biocontainers/seqkit:0.15.0--0"
-    }
+    container "quay.io/biocontainers/seqkit:0.15.0--0"
 
     input:
         tuple val(meta), path(reads)
diff --git a/modules/local/seqprep/adapter_trimming/main.nf b/modules/local/seqprep/adapter_trimming/main.nf
index 5818496..4c09ed1 100644
--- a/modules/local/seqprep/adapter_trimming/main.nf
+++ b/modules/local/seqprep/adapter_trimming/main.nf
@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/local/seqprep/read_merging/main.nf b/modules/local/seqprep/read_merging/main.nf
index 964f2fa..c258d96 100644
--- a/modules/local/seqprep/read_merging/main.nf
+++ b/modules/local/seqprep/read_merging/main.nf
@@ -11,11 +11,7 @@ process SEQPREP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }    conda (params.enable_conda ? "bioconda::seqprep=1.3.2" : null)
 
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/seqprep:1.3.2--h5bf99c6_5"
-    } else {
-        container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
-    }
+    container "quay.io/biocontainers/seqprep:1.3.2--h5bf99c6_5"
 
     input:
     tuple val(meta), path(reads)