diff --git a/eva_submission/eload_brokering.py b/eva_submission/eload_brokering.py
index d085ea5..dff819d 100644
--- a/eva_submission/eload_brokering.py
+++ b/eva_submission/eload_brokering.py
@@ -12,7 +12,7 @@
 from eva_submission.ENA_submission.upload_to_ENA import ENAUploader, ENAUploaderAsync
 from eva_submission.biosample_submission.biosamples_submitters import SampleMetadataSubmitter, SampleReferenceSubmitter
 from eva_submission.eload_submission import Eload
-from eva_submission.eload_utils import read_md5
+from eva_submission.eload_utils import read_md5, get_nextflow_config_flag
 from eva_submission.submission_config import EloadConfig
 
 
@@ -169,7 +169,7 @@ def _run_brokering_prep_workflow(self):
             'output_dir': output_dir,
             'executable': cfg['executable']
         }
-        # run the validation
+        # run the brokering preparation
         brokering_config_file = os.path.join(self.eload_dir, 'brokering_config_file.yaml')
         with open(brokering_config_file, 'w') as open_file:
             yaml.safe_dump(brokering_config, open_file)
@@ -180,7 +180,8 @@ def _run_brokering_prep_workflow(self):
                 ' '.join((
                     cfg['executable']['nextflow'], brokering_script,
                     '-params-file', brokering_config_file,
-                    '-work-dir', output_dir
+                    '-work-dir', output_dir,
+                    get_nextflow_config_flag()
                 ))
             )
         except subprocess.CalledProcessError as e:
diff --git a/eva_submission/eload_ingestion.py b/eva_submission/eload_ingestion.py
index 1072509..9fff9df 100644
--- a/eva_submission/eload_ingestion.py
+++ b/eva_submission/eload_ingestion.py
@@ -21,7 +21,8 @@
 
 from eva_submission import NEXTFLOW_DIR
 from eva_submission.eload_submission import Eload
-from eva_submission.eload_utils import provision_new_database_for_variant_warehouse, check_project_exists_in_evapro
+from eva_submission.eload_utils import provision_new_database_for_variant_warehouse, check_project_exists_in_evapro, \
+    get_nextflow_config_flag
 from eva_submission.submission_config import EloadConfig
 from eva_submission.vep_utils import get_vep_and_vep_cache_version
 
@@ -684,7 +685,8 @@ def run_nextflow(self, workflow_name, params, resume, tasks=all_tasks):
                     cfg['executable']['nextflow'], nextflow_script,
                     '-params-file', params_file,
                     '-work-dir', work_dir,
-                    '-resume' if resume else ''
+                    '-resume' if resume else '',
+                    get_nextflow_config_flag()
                 ))
             )
             shutil.rmtree(work_dir)
diff --git a/eva_submission/eload_utils.py b/eva_submission/eload_utils.py
index 0e7b748..3e151ef 100644
--- a/eva_submission/eload_utils.py
+++ b/eva_submission/eload_utils.py
@@ -45,6 +45,7 @@ def is_single_insdc_sequence(reference_accession):
     return not NCBIAssembly.is_assembly_accession_format(reference_accession) and \
            NCBISequence.is_genbank_accession_format(reference_accession)
 
+
 def resolve_accession_from_text(reference_text):
     """
     :param reference_text:
@@ -262,3 +263,14 @@ def create_assembly_report_from_fasta(assembly_fasta_path):
             open_file.write('\t'.join(['na', 'na', 'na', 'na', contig_name, '<>', 'na', 'na', str(seq_length), 'na']) + '\n')
     return assembly_report_path
 
+
+def get_nextflow_config_flag():
+    """
+    Return the commandline flag for Nextflow to use the config provided in environment variable SUBMISSION_NEXTFLOW_CONFIG.
+    If not provided, return an empty string, which allows Nextflow to use the default precedence as described here:
+    https://www.nextflow.io/docs/latest/config.html
+    """
+    env_val = os.getenv('SUBMISSION_NEXTFLOW_CONFIG')
+    if env_val:
+        return f'-c {env_val}'
+    return ''
diff --git a/eva_submission/eload_validation.py b/eva_submission/eload_validation.py
index 2378c54..12b5e38 100755
--- a/eva_submission/eload_validation.py
+++ b/eva_submission/eload_validation.py
@@ -13,7 +13,7 @@
 
 from eva_submission import NEXTFLOW_DIR
 from eva_submission.eload_submission import Eload
-from eva_submission.eload_utils import resolve_single_file_path, detect_vcf_aggregation
+from eva_submission.eload_utils import resolve_single_file_path, detect_vcf_aggregation, get_nextflow_config_flag
 from eva_submission.samples_checker import compare_spreadsheet_and_vcf
 from eva_submission.xlsx.xlsx_validation import EvaXlsxValidator
 
@@ -254,8 +254,8 @@ def _run_validation_workflow(self, validation_tasks):
             'validation_tasks': validation_tasks
         }
         # run the validation
-        validation_confg_file = os.path.join(self.eload_dir, 'validation_confg_file.yaml')
-        with open(validation_confg_file, 'w') as open_file:
+        validation_config_file = os.path.join(self.eload_dir, 'validation_config_file.yaml')
+        with open(validation_config_file, 'w') as open_file:
             yaml.safe_dump(validation_config, open_file)
         validation_script = os.path.join(NEXTFLOW_DIR, 'validation.nf')
         try:
@@ -264,8 +264,9 @@ def _run_validation_workflow(self, validation_tasks):
                 ' '.join((
                     'export NXF_OPTS="-Xms1g -Xmx8g"; ',
                     cfg['executable']['nextflow'], validation_script,
-                    '-params-file', validation_confg_file,
-                    '-work-dir', output_dir
+                    '-params-file', validation_config_file,
+                    '-work-dir', output_dir,
+                    get_nextflow_config_flag()
                 ))
             )
         except subprocess.CalledProcessError:
diff --git a/eva_submission/nextflow/accession_and_load.nf b/eva_submission/nextflow/accession_and_load.nf
index 2f17782..2086ca9 100644
--- a/eva_submission/nextflow/accession_and_load.nf
+++ b/eva_submission/nextflow/accession_and_load.nf
@@ -168,6 +168,7 @@ workflow {
 * Convert the genome to the same naming convention as the VCF
 */
 process prepare_genome {
+    label 'default_time', 'med_mem'
 
     input:
     tuple path(fasta), path(report), val(assembly_accession), path(vcf_files)
@@ -189,6 +190,8 @@ process prepare_genome {
 * Normalise the VCF files
 */
 process normalise_vcf {
+    label 'default_time', 'med_mem'
+
     input:
     tuple val(vcf_filename), path(fasta), path(vcf_file), path(csi_file)
 
@@ -208,11 +211,10 @@ process normalise_vcf {
  * Accession VCFs
  */
 process accession_vcf {
-    clusterOptions "-g /accession/instance-${params.instance_id} \
-                    -o $params.logs_dir/${log_filename}.log \
-                    -e $params.logs_dir/${log_filename}.err"
+    label 'long_time', 'med_mem'
 
-    memory '6.7 GB'
+    clusterOptions "-o $params.logs_dir/${log_filename}.log \
+                    -e $params.logs_dir/${log_filename}.err"
 
     input:
     tuple val(vcf_filename), val(vcf_file), val(assembly_accession), val(aggregation), val(fasta), val(report)
@@ -236,7 +238,7 @@ process accession_vcf {
 
 
     """
-    (java -Xmx6g -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || \
+    (java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.accession_pipeline --spring.config.location=file:$params.accession_job_props $pipeline_parameters) || \
     # If accessioning fails due to missing variants, but the only missing variants are structural variants,
     # then we should treat this as a success from the perspective of the automation.
     # TODO revert once accessioning pipeline properly registers structural variants
@@ -251,6 +253,8 @@ process accession_vcf {
  * Sort and compress accessioned VCFs
  */
 process sort_and_compress_vcf {
+    label 'default_time', 'med_mem'
+
     publishDir params.public_dir,
 	mode: 'copy'
 
@@ -269,6 +273,8 @@ process sort_and_compress_vcf {
 
 
 process csi_index_vcf {
+    label 'default_time', 'small_mem'
+
     publishDir params.public_dir,
 	mode: 'copy'
 
@@ -288,7 +294,7 @@ process csi_index_vcf {
  * Copy files from eva_public to FTP folder.
  */
  process copy_to_ftp {
-    label 'datamover'
+    label 'datamover', 'short_time', 'small_mem'
 
     input:
     // ensures that all indices are done before we copy
@@ -316,6 +322,8 @@ process csi_index_vcf {
  * Load into variant db.
  */
 process load_variants_vcf {
+    label 'long_time', 'med_mem'
+
     clusterOptions {
         return "-o $params.logs_dir/load_variants.${vcf_filename}.log \
                 -e $params.logs_dir/load_variants.${vcf_filename}.err"
@@ -327,8 +335,6 @@ process load_variants_vcf {
     output:
     val true, emit: variant_load_complete
 
-    memory '5 GB'
-
     script:
     def pipeline_parameters = " --spring.batch.job.names=load-vcf-job"
     pipeline_parameters += " --input.vcf.aggregation=" + aggregation.toString().toUpperCase()
@@ -338,7 +344,7 @@ process load_variants_vcf {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -347,6 +353,8 @@ process load_variants_vcf {
  * Run VEP using eva-pipeline.
  */
 process run_vep_on_variants {
+    label 'long_time', 'med_mem'
+
     clusterOptions {
         return "-o $params.logs_dir/annotation.${analysis_accession}.log \
                 -e $params.logs_dir/annotation.${analysis_accession}.err"
@@ -362,8 +370,6 @@ process run_vep_on_variants {
     output:
     val true, emit: vep_run_complete
 
-    memory '5 GB'
-
     script:
     def pipeline_parameters = ""
 
@@ -380,7 +386,7 @@ process run_vep_on_variants {
     pipeline_parameters += " --app.vep.cache.species=" + vep_species.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -390,6 +396,8 @@ process run_vep_on_variants {
  * Calculate statistics using eva-pipeline.
  */
 process calculate_statistics_vcf {
+    label 'long_time', 'med_mem'
+
     clusterOptions {
         return "-o $params.logs_dir/statistics.${analysis_accession}.log \
                 -e $params.logs_dir/statistics.${analysis_accession}.err"
@@ -406,12 +414,9 @@ process calculate_statistics_vcf {
     output:
     val true, emit: statistics_calc_complete
 
-    memory '5 GB'
-
     script:
     def pipeline_parameters = ""
 
-
     pipeline_parameters += " --spring.batch.job.names=calculate-statistics-job"
 
     pipeline_parameters += " --input.vcf.aggregation=" + aggregation.toString().toUpperCase()
@@ -421,7 +426,7 @@ process calculate_statistics_vcf {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.load_job_props --parameters.path=$params.load_job_props $pipeline_parameters
     """
 }
 
@@ -429,6 +434,8 @@ process calculate_statistics_vcf {
  * Import Accession Into Variant warehouse
  */
 process import_accession {
+    label 'default_time', 'med_mem'
+
     clusterOptions {
         log_filename = vcf_file.getFileName().toString()
         return "-o $params.logs_dir/acc_import.${log_filename}.log \
@@ -440,8 +447,6 @@ process import_accession {
     val all_accession_complete
     val variant_load_output
 
-    memory '5 GB'
-
     script:
     def pipeline_parameters = ""
 
@@ -451,6 +456,6 @@ process import_accession {
     pipeline_parameters += " --spring.data.mongodb.database=" + db_name.toString()
 
     """
-    java -Xmx4G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.acc_import_job_props --parameters.path=$params.acc_import_job_props $pipeline_parameters
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.eva_pipeline --spring.config.location=file:$params.acc_import_job_props --parameters.path=$params.acc_import_job_props $pipeline_parameters
     """
 }
diff --git a/eva_submission/nextflow/prepare_brokering.nf b/eva_submission/nextflow/prepare_brokering.nf
index f116bc6..7ea4334 100644
--- a/eva_submission/nextflow/prepare_brokering.nf
+++ b/eva_submission/nextflow/prepare_brokering.nf
@@ -62,6 +62,7 @@ workflow {
 * Compress the VCF file
 */
 process compress_vcf {
+    label 'default_time', 'small_mem'
 
     input:
     path vcf_file
@@ -85,6 +86,7 @@ process compress_vcf {
 * Index the compressed VCF file
 */
 process csi_index_vcf {
+    label 'default_time', 'small_mem'
 
     input:
     tuple val(input_vcf), path(compressed_vcf)
@@ -101,6 +103,7 @@ process csi_index_vcf {
 * Convert the genome to the same naming convention as the VCF
 */
 process prepare_genome {
+    label 'default_time', 'med_mem'
 
     input:
     tuple path(fasta), path(report), val(assembly_accession), path(vcf_files)
@@ -122,6 +125,8 @@ process prepare_genome {
 * Normalise the VCF files
 */
 process normalise_vcf {
+    label 'default_time', 'med_mem'
+
     publishDir "$params.output_dir",
             overwrite: false,
             mode: "copy",
@@ -148,6 +153,7 @@ process normalise_vcf {
 * md5 the compressed vcf and its index
 */
 process md5_vcf_and_index {
+    label 'short_time', 'small_mem'
 
     publishDir "$params.output_dir",
             overwrite: true,
diff --git a/eva_submission/nextflow/remap_and_cluster.nf b/eva_submission/nextflow/remap_and_cluster.nf
index 59d0db8..fca924a 100644
--- a/eva_submission/nextflow/remap_and_cluster.nf
+++ b/eva_submission/nextflow/remap_and_cluster.nf
@@ -25,7 +25,6 @@ def helpMessage() {
 params.source_assemblies = null
 params.target_assembly_accession = null
 params.species_name = null
-params.memory = 8
 params.logs_dir = null
 // help
 params.help = null
@@ -46,6 +45,8 @@ if (!params.taxonomy_id || !params.source_assemblies || !params.target_assembly_
 
 
 process retrieve_source_genome {
+    label 'short_time', 'med_mem'
+
     when:
     source_assembly_accession != params.target_assembly_accession
 
@@ -65,6 +66,7 @@ process retrieve_source_genome {
 
 
 process retrieve_target_genome {
+    label 'short_time', 'med_mem'
 
     input:
     val target_assembly_accession
@@ -82,6 +84,7 @@ process retrieve_target_genome {
 }
 
 process update_source_genome {
+    label 'short_time', 'med_mem'
 
     input:
     tuple val(source_assembly_accession), path(source_fasta), path(source_report)
@@ -96,6 +99,7 @@ process update_source_genome {
 }
 
 process update_target_genome {
+    label 'short_time', 'med_mem'
 
     input:
     path target_fasta
@@ -116,8 +120,7 @@ process update_target_genome {
  * Extract the submitted variants to remap from the accessioning warehouse and store them in a VCF file.
  */
 process extract_vcf_from_mongo {
-    memory "${params.memory}GB"
-    clusterOptions "-g /accession"
+    label 'long_time', 'med_mem'
 
     when:
     source_assembly_accession != params.target_assembly_accession
@@ -133,7 +136,7 @@ process extract_vcf_from_mongo {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.vcf_extractor \
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.vcf_extractor \
         --spring.config.location=file:${params.extraction_properties} \
         --parameters.assemblyAccession=${source_assembly_accession} \
         --parameters.fasta=${source_fasta} \
@@ -147,7 +150,7 @@ process extract_vcf_from_mongo {
  * Variant remapping pipeline
  */
 process remap_variants {
-    memory "${params.memory}GB"
+    label 'long_time', 'med_mem'
 
     input:
     tuple val(source_assembly_accession), path(source_fasta), path(source_vcf)
@@ -184,8 +187,7 @@ process remap_variants {
  * Ingest the remapped submitted variants from a VCF file into the accessioning warehouse.
  */
 process ingest_vcf_into_mongo {
-    memory "${params.memory}GB"
-    clusterOptions "-g /accession"
+    label 'long_time', 'med_mem'
 
     input:
     tuple val(source_assembly_accession), path(remapped_vcf)
@@ -198,7 +200,7 @@ process ingest_vcf_into_mongo {
 
     script:
     """
-    java -Xmx8G -jar $params.jar.vcf_ingestion \
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.vcf_ingestion \
         --spring.config.location=file:${params.ingestion_properties} \
         --parameters.remappedFrom=${source_assembly_accession} \
         --parameters.vcf=${remapped_vcf} \
@@ -212,8 +214,7 @@ process ingest_vcf_into_mongo {
  * Cluster target assembly.
  */
 process cluster_studies_from_mongo {
-    memory "${params.memory}GB"
-    clusterOptions "-g /accession/instance-${params.clustering_instance}"
+    label 'long_time', 'med_mem'
 
     input:
     path ingestion_log
@@ -225,7 +226,7 @@ process cluster_studies_from_mongo {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --spring.batch.job.names=STUDY_CLUSTERING_JOB \
         > ${params.target_assembly_accession}_clustering.log
@@ -236,8 +237,7 @@ process cluster_studies_from_mongo {
  * Run clustering QC job
  */
 process qc_clustering {
-    memory "${params.memory}GB"
-    clusterOptions "-g /accession"
+    label 'long_time', 'med_mem'
 
     input:
     path rs_report
@@ -248,7 +248,7 @@ process qc_clustering {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --spring.batch.job.names=NEW_CLUSTERED_VARIANTS_QC_JOB \
         > ${params.target_assembly_accession}_clustering_qc.log
@@ -260,8 +260,7 @@ process qc_clustering {
  * Run Back propagation of new clustered RS only if the remapping was performed
  */
 process backpropagate_clusters {
-    memory "${params.memory}GB"
-    clusterOptions "-g /accession"
+    label 'long_time', 'med_mem'
 
     input:
     tuple val(source_assembly_accession), path(remapped_vcf)
@@ -273,7 +272,7 @@ process backpropagate_clusters {
     publishDir "$params.logs_dir", overwrite: true, mode: "copy", pattern: "*.log*"
 
     """
-    java -Xmx8G -jar $params.jar.clustering \
+    java -Xmx${task.memory.toGiga()-1}G -jar $params.jar.clustering \
         --spring.config.location=file:${params.clustering_properties} \
         --parameters.remappedFrom=${source_assembly_accession} \
         --spring.batch.job.names=BACK_PROPAGATE_NEW_RS_JOB \
@@ -286,7 +285,7 @@ workflow {
         species_name = params.species_name.toLowerCase().replace(" ", "_")
 
         remapping_required = params.source_assemblies.any {it != params.target_assembly_accession}
-        if (remapping_required){
+        if (remapping_required) {
             retrieve_source_genome(params.source_assemblies, species_name)
             retrieve_target_genome(params.target_assembly_accession, species_name)
             update_source_genome(retrieve_source_genome.out.source_assembly, params.remapping_config)
@@ -300,7 +299,7 @@ workflow {
             // to make sure it does not run out of values when multiple remapping are performed
             // See https://www.nextflow.io/docs/latest/process.html#multiple-input-channels
             backpropagate_clusters(remap_variants.out.remapped_vcfs, qc_clustering.out.clustering_qc_log_filename)
-        }else{
+        } else {
             // We're using params.genome_assembly_dir because cluster_studies_from_mongo needs to receive a file object
             cluster_studies_from_mongo(params.genome_assembly_dir)
             qc_clustering(cluster_studies_from_mongo.out.rs_report_filename)
diff --git a/eva_submission/nextflow/validation.nf b/eva_submission/nextflow/validation.nf
index ed3e1e8..42e5762 100644
--- a/eva_submission/nextflow/validation.nf
+++ b/eva_submission/nextflow/validation.nf
@@ -54,6 +54,8 @@ workflow {
 * Validate the VCF file format
 */
 process check_vcf_valid {
+    label 'long_time', 'med_mem'
+
     publishDir "$params.output_dir",
             overwrite: false,
             mode: "copy"
@@ -80,6 +82,8 @@ process check_vcf_valid {
 * Validate the VCF reference allele
 */
 process check_vcf_reference {
+    label 'long_time', 'med_mem'
+
     publishDir "$params.output_dir",
             overwrite: true,
             mode: "copy"
@@ -106,6 +110,8 @@ process check_vcf_reference {
  * Detect the structural variant in VCF
  */
 process detect_sv {
+    label 'default_time', 'med_mem'
+
     publishDir "$params.output_dir",
             overwrite: false,
             mode: "copy"
diff --git a/tests/nextflow-tests/nextflow.config b/tests/nextflow-tests/nextflow.config
index 873d076..19648d4 100644
--- a/tests/nextflow-tests/nextflow.config
+++ b/tests/nextflow-tests/nextflow.config
@@ -1,5 +1,9 @@
 process {
-  executor='local'
+  executor = 'local'
+
+  time = '30m'
+  memory = '5 GB'
+  
   withLabel: datamover {
     tag = 'data movement happens in this process'
   }
diff --git a/tests/test_eload_brokering.py b/tests/test_eload_brokering.py
index 80be290..f7f0772 100644
--- a/tests/test_eload_brokering.py
+++ b/tests/test_eload_brokering.py
@@ -106,7 +106,7 @@ def test_run_brokering_prep_workflow(self):
             self.eload._run_brokering_prep_workflow()
         m_execute.assert_called_once_with(
             'Nextflow brokering preparation process',
-            f'path_to_nextflow {nf_script} -params-file {config_file} -work-dir {temp_dir}'
+            f'path_to_nextflow {nf_script} -params-file {config_file} -work-dir {temp_dir} '
         )
 
     def test_parse_bcftools_norm_report(self):
diff --git a/tests/test_eload_ingestion.py b/tests/test_eload_ingestion.py
index d85bff7..da1bae5 100644
--- a/tests/test_eload_ingestion.py
+++ b/tests/test_eload_ingestion.py
@@ -592,8 +592,7 @@ def _post_run_nextflow_assert(self, m_run_command, workflow_name, work_dir, resu
         command = (f'export NXF_OPTS="-Xms1g -Xmx8g";  '
                    f'/path/to/nextflow {nextflow_script} -params-file {self.eload.project_dir}/workflow_params.yaml '
                    f'-work-dir {work_dir} ')
-        if resume:
-            command += '-resume'
+        command += '-resume ' if resume else ' '
         m_run_command.assert_called_once_with('Nextflow workflow process', command)
         with open(os.path.join(self.eload.project_dir, 'workflow_params.yaml')) as open_file:
             params = yaml.safe_load(open_file)