diff --git a/bin/compare_busco.py b/bin/compare_busco.py
new file mode 100755
index 0000000..d49f983
--- /dev/null
+++ b/bin/compare_busco.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+
+import argparse
+import json
+from typing import Tuple
+
+def parse_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "json_files",
+        metavar="FILE",
+        type=str,
+        nargs="+",
+        help="Paths to one or more BUSCO JSON files"
+    )
+    return parser.parse_args()
+
+def get_complete_buscos(json_file) -> Tuple[str, float]:
+    """
+    Get the assembler name and complete BUSCO % from a json
+    """
+    with open(json_file, 'r') as f:
+        j = json.load(f)
+        assembler = j['parameters']['out']
+        # get assembler only from e.g. barcode01_consensus_busco
+        assembler = assembler.split('_')[1]
+        assert assembler in ['flye', 'unicycler', 'consensus']
+        complete_busco = j['results']['Complete percentage']
+        return assembler, complete_busco
+
+if __name__ == "__main__":
+    args = parse_args()
+    results = [get_complete_buscos(file) for file in args.json_files]
+    highest_busco = max(results, key=lambda x: x[1])
+    print(highest_busco[0], end="") # don't print newline
diff --git a/main.nf b/main.nf
index 4e98c84..9ad7bed 100755
--- a/main.nf
+++ b/main.nf
@@ -6,6 +6,7 @@ nextflow.enable.dsl=2
 // Import processes or subworkflows to be run in the workflow
 include { check_input } from './modules/check_input'
 include { check_samplesheet } from './modules/check_samplesheet'
+include { concat_fastas } from './modules/concat_fa'
 include { concat_fastqs } from './modules/run_pigz'
 include { porechop } from './modules/run_porechop' 
 include { pycoqc_summary } from './modules/run_pycoqc'
@@ -26,22 +27,17 @@ include { select_assembly } from './modules/select_assembly'
 include { trycycler_msa } from './modules/run_trycycler_msa'
 include { trycycler_partition } from './modules/run_trycycler_partition'
 include { trycycler_consensus} from './modules/run_trycycler_consensus'
+include { medaka_polish_denovo } from './modules/run_medaka_polish_denovo'
 include { medaka_polish_consensus } from './modules/run_medaka_polish_consensus'
-include { medaka_polish_flye } from './modules/run_medaka_polish_flye'
 include { plassembler } from './modules/run_plassembler'
 include { bakta_annotation_plasmids } from './modules/run_bakta_annotation_plasmids'
 include { busco_annotation_plasmids } from './modules/run_busco_annotation_plasmids'
 include { quast_qc_chromosomes } from './modules/run_quast_qc_chromosomes'
-include { quast_qc_flye_chromosomes } from './modules/run_quast_qc_flye_chromosomes'
 include { bakta_annotation_chromosomes } from './modules/run_bakta_annotation_chromosomes'
-include { bakta_annotation_flye_chromosomes } from './modules/run_bakta_annotation_flye_chromosomes'
-include { busco_annotation_chromosomes } from './modules/run_busco_annotation_chromosomes'
-include { busco_annotation_flye_chromosomes } from './modules/run_busco_annotation_flye_chromosomes'
+include { busco_qc_chromosomes } from './modules/run_busco_qc_chromosomes'
 include { abricateVFDB_annotation_chromosomes } from './modules/run_abricateVFDB_annotation_chromosomes'
-include { abricateVFDB_annotation_flye_chromosomes } from './modules/run_abricateVFDB_annotation_flye_chromosomes'
 include { abricateVFDB_annotation_reference } from './modules/run_abricateVFDB_annotation_reference'
 include { amrfinderplus_annotation_chromosomes } from './modules/run_amrfinderplus_annotation_chromosomes'
-include { amrfinderplus_annotation_flye_chromosomes } from './modules/run_amrfinderplus_annotation_flye_chromosomes'
 include { create_samplesheet_for_processed } from './modules/create_samplesheet_for_processed'
 include { create_phylogeny_tree_related_files } from './modules/create_phylogeny_tree_related_files'
 include { run_orthofinder } from './modules/run_orthofinder'
@@ -187,10 +183,8 @@ if ( params.help || (!params.input_directory && !params.samplesheet) || !params.
   // SCREEN FOR CONTAMINANTS 
   kraken2(porechop.out.trimmed_fq, kraken2_db)
 
-  // ASSEMBLE GENOME WITH FLYE
+  // DE NOVO GENOME ASSEMBLIES
   flye_assembly(porechop.out.trimmed_fq)
-
-  // ASSEMBLE GENOME WITH UNICYCLER
   unicycler_assembly(porechop.out.trimmed_fq)
 
   // DETECT PLASMIDS AND OTHER MOBILE ELEMENTS 
@@ -200,296 +194,290 @@ if ( params.help || (!params.input_directory && !params.samplesheet) || !params.
                   
   plassembler(plassembler_in, get_plassembler.out.plassembler_db)
 
-  // CLUSTER CONTIGS WITH TRYCYCLER 
-  combined_assemblies = unicycler_assembly.out.unicycler_assembly
-                .join(flye_assembly.out.flye_assembly, by:0)
-                .join(porechop.out.trimmed_fq, by:0)
-                .map { barcode, unicycler_assembly, flye_assembly, trimmed_fq ->
-                  tuple(barcode, unicycler_assembly, flye_assembly, trimmed_fq)}
-
-  trycycler_cluster(combined_assemblies)
-
-  /* 
-   * Building a tree requires >2 contigs.
-   * Use `contigs.phylip` to check the number of contigs. The number of lines
-   * in a `.phylip` indicates the number of contigs/tips.
-   */ 
-  assemblies_with_trycycler_clusters = trycycler_cluster.out.trycycler_cluster 
-    .map { barcode, assemblies, cluster_phylip ->
-        def phylip_lines = cluster_phylip.text.readLines().size() - 1 // Exclude header
-        return [barcode, assemblies, phylip_lines] 
+  /*
+   * CONSENSUS ASSEMBLY PRE-PROCESSING
+   * 
+   * Trycycler requires >= 3 contigs to run. Use the in-built .countFasta()
+   * operator to count the total number of contigs assembled for each barcode.
+   *
+   * If additional assemblers/read subsets/replicates are added, ensure it 
+   * is added here.
+   */
+  num_contigs_per_barcode =
+    unicycler_assembly.out.unicycler_assembly
+    .mix(flye_assembly.out.flye_assembly)
+    .map { barcode, assembly_dir ->
+        // Count num contigs per assembly
+        def fa = assembly_dir + "/assembly.fasta"
+        def ncontigs = fa.countFasta()
+        return [barcode, ncontigs]
     }
-    .branch { barcode, assemblies, phylip_lines ->
-        run_trycycler: phylip_lines >= 3 // Enough clusters/contigs
-        skip_trycycler: phylip_lines < 3
+    .groupTuple()
+    .map { barcode, ncontigs ->
+        // Add total contigs across assemblies
+        def total_contigs = ncontigs[0].toInteger() + ncontigs[1].toInteger()
+        return [barcode, total_contigs]
+    }
+
+  denovo_assemblies =
+    unicycler_assembly.out.unicycler_assembly
+    .join(flye_assembly.out.flye_assembly, by:0)
+    .join(porechop.out.trimmed_fq, by:0)
+    .join(num_contigs_per_barcode, by:0)
+
+  denovo_assembly_contigs =
+    denovo_assemblies
+    .branch { barcode, unicycler, flye, trimmed_fq, num_contigs ->
+        run_trycycler: num_contigs >= 3
+        skip_trycycler: num_contigs < 3
     }
 
   trycycler_skipped_barcodes =
     // barcodes with insufficient contigs for trycycler
-    assemblies_with_trycycler_clusters.skip_trycycler
-    .map { barcode, assemblies, phylip_lines -> barcode }
+    // TODO: Remove this when select_assembly is revised.
+    // denovo_assemblies can be passed directly when ready.
+    denovo_assembly_contigs.skip_trycycler
+    .map { 
+        barcode, unicycler_assembly, flye_assembly, trimmed_fq, num_contigs -> barcode
+    }
     .collect()
 
   // RUN TRYCYCLER (CONSENSUS ASSEMBLY) IF SUFFICIENT # CONTIGS
-  // CLASSIFY CONTIGS WITH TRYCYCLER
-  classify_trycycler(assemblies_with_trycycler_clusters.run_trycycler)
-
-  // RECONCILE CONTIGS WITH TRYCYCLER
-  contigs_to_reconcile = classify_trycycler.out.reconcile_contigs
-                      .join(porechop.out.trimmed_fq, by: 0)
-                      .flatMap { barcode, reconcile_contigs, trimmed_fq ->
-                        if (reconcile_contigs instanceof List) {
-                          reconcile_contigs.collect { cluster_dir ->
-                            tuple(barcode, cluster_dir, trimmed_fq)
-                          }
-                        } else {
-                          [tuple(barcode, reconcile_contigs, trimmed_fq)]
-                        }
-                      }
-
-  trycycler_reconcile(contigs_to_reconcile)
-
-  /*
-   * SELECT "BEST" ASSEMBLY (CONSENSUS (TRYCYCLER) OR FLYE)
-   *    TODO: Revise reference-free approach 
-   *    TODO: Include unicycler assembly too
-   */
-  trycycler_reconciled = 
-    // Channel for successful trycycler assemblies
-    trycycler_reconcile.out.reconciled_seqs
-    .groupTuple(by:[0])
-  
-  select_in = trycycler_reconcile.out.reconciled_seqs
-              .groupTuple(by:[0])
-              .join(flye_assembly.out.flye_assembly, by:0)
-              .join(kraken2.out.kraken2_screen, by:0)
-              .map { barcode, reconciled, flye_assembly, k2_report ->
-                  tuple(barcode, reconciled, flye_assembly, k2_report)}
-
-  select_assembly(select_in, get_ncbi.out.ncbi_lookup)	
-
-  // IF CONSENSUS ASSEMBLY IS BEST...
-
-  // TRYCYCLER MULTIPLE SEQUENCE ALIGNMENT
-  // CONSENSUS APPROACH : Check if file Consensus.txt exists
-  msa_in_consensus = select_assembly.out.consensus_good
-          .filter { it[1].exists() }  // Ensure the correct path is checked for existence
-          .flatMap { tuple ->
-            def barcode = tuple[0]
-            def consensus_file = tuple[1]
-            def final_path = tuple[2]
-            if (final_path instanceof List) {
-                // If final_path is a list, return a stream of separate tuples
-                final_path.collect { path ->
-                    [barcode, consensus_file, path]
-                }
-            } else {
-                // If final_path is not a list, return a single-element list with the original tuple
-                [[barcode, consensus_file, final_path]]
-            }
-          }
-          
-  trycycler_msa(msa_in_consensus)
-  trycycler_msa_out = trycycler_msa.out.three_msa
-
-  // TRYCYCLER PARTITIONING READS
-  partition_in = select_assembly.out.consensus_good
-          .filter { it[1].exists() }  // Ensure the correct path is checked for existence
-          .join(porechop.out.trimmed_fq, by: 0)
-  	  .map { barcode, consensus_file, final_path, trimmed_fq ->
-            tuple(barcode, consensus_file, final_path, trimmed_fq)
-          }
-
-  trycycler_partition(partition_in)
-
-  // TRYCYCLER CONSENSUS
-  partition_out_raw = trycycler_partition.out.four_reads
-
-  partition_out = partition_out_raw.flatMap { barcode, path ->
-    def directory = new File(path.toString())
-    def files = directory.listFiles().findAll { it.name.endsWith('_reconciled') }
-    files.collect { file -> [barcode, "${barcode}_${file.name}", file.path] }
-  }
-
-// TODO MAKE NAMING CONSISTENT WITH OTHER CHANNELS
-  consensus_in = trycycler_msa_out
-  		 .join(partition_out, by:1)
-                 .map { row ->
-                     [row[1], row[0], row[2], row[4]]
-                 }
-
-  trycycler_consensus(consensus_in)
-
-  // MEDAKA POLISH CONSENSUS ASSEMBLY
-  // TODO MAKE NAMING CONSISTENT WITH OTHER CHANNELS
-  consensus_polish_in = partition_out
-                        .join(trycycler_consensus.out.consensus_consensus, by:1)
-			                  .map { row ->[row[1], row[0], row[2], row[4]]}
-
-  medaka_polish_consensus(consensus_polish_in)
-
-  // ANNOTATE VARIOUS CONSENSUS-CHROMOSOME FEATURES  
-  // TODO MAKE NAMING CONSISTENT WITH OTHER CHANNELS
-  polish_grouped_by_barcode = medaka_polish_consensus.out.consensus_polished
-			.groupTuple(by:[0])
-			.map { row -> [row[0], row[2]]}
-
-  // QUAST QC CONSENSUS-ASSEMBLY
-  quast_qc_chromosomes(polish_grouped_by_barcode)
-
-  // BAKTA ANNOTATE GENE FEATURES 
-  bakta_annotation_chromosomes(polish_grouped_by_barcode,get_bakta.out.bakta_db)
-
-  // BUSCO ANNOTATE CONSENSUS-CHROMOSOME FEATURES
-  busco_annotation_chromosomes(bakta_annotation_chromosomes.out.bakta_annotations, get_busco.out.busco_db) 
-
-  // AMRFINDERPLUS ANNOTATE CONSENSUS-CHROMOSOME AMR-GENES
-  amrfinderplus_annotation_chromosomes(bakta_annotation_chromosomes.out.bakta_annotations,
-                                        get_amrfinderplus.out.amrfinderplus_db)
-  
-  // ABRICATE ANNOTATE CONSENSUS-CHROMOSOME WITH VFDB-GENES
-  abricateVFDB_annotation_chromosomes(polish_grouped_by_barcode)
-
-  consensus_processed_samples=amrfinderplus_annotation_chromosomes.out.map { it[0] }.collect()
+  // TRYCYCLER: Cluster contigs
+  trycycler_cluster(denovo_assembly_contigs.run_trycycler)
+
+  barcode_cluster_sizes =
+    // trycycler_cluster filters out small contigs (default < 5000nt) and can
+    // result in < 2 contigs here again. Use the same branching logic to avoid
+    // < 2 contig errors.
+    trycycler_cluster.out.phylip
+    .map { barcode, contigs_phylip ->
+        def phylip_lines = contigs_phylip.text.readLines().size - 1 // exclude header
+        return [barcode, phylip_lines]
+    }
+    .branch { barcode, phylip_lines ->
+        run_trycycler: phylip_lines >= 3
+        skip_trycycler: phylip_lines < 3
+        // create a channel from skip_trycycler if failed barcodes need to be reported/used
+    }
 
-  // IF FLYE ASSEMBLY IS BEST...
+  // TRYCYCLER: Classify clusters
+  clusters_to_classify =
+    // Add path to clusters with sufficient contigs
+    trycycler_cluster.out.clusters
+    .join(barcode_cluster_sizes.run_trycycler)
 
-  /*
-   * Channel that has the ids for all samples that either:
-   *  1. Has too few contigs for trycycler/consensus assembly
-   *  2. Enough contigs but flye > consensus assembly
-   *
-   * flye_better_barcode channel emits each sample id separately for joining
-   * with the paths to the flye assembly and trimmed fqs later
-   * 
-   */
-  flye_better_barcodes = select_assembly.out.consensus_discard
-    .map { barcode, consensus_file, filtered_flye_contigs -> barcode }
-    .mix(trycycler_skipped_barcodes)
-    .flatMap()
+  classify_trycycler(clusters_to_classify)
 
-  /*
-   * MEDAKA-POLISH FLYE ASSEMBLY 
-   *
-   * The current select_assembly process discards any non-chromosomal
-   * contigs based on a reference-based NCBI lookup.
-   *
-   * The following channel passes in ALL contigs assembled by flye for
-   * polishing as select_assembly is revised. i.e. not just the putatively
-   * chromosmal ones.
-   *
-   */
-  flye_polish_in =
-    flye_better_barcodes
-    .join(flye_assembly.out.flye_assembly, by: 0)
+  // TRYCYCLER: Reconcile contigs
+  clusters_to_reconcile_flat = 
+    classify_trycycler.out.clusters_to_reconcile
     .join(porechop.out.trimmed_fq, by: 0)
+    // from [barcode, [pathA, pathB], ...]
+    // to [barcode, pathA, ...]; [barcode, pathB, ...]
+    .transpose()
+
+  trycycler_reconcile(clusters_to_reconcile_flat)
+
+  reconciled_cluster_dirs = 
+    trycycler_reconcile.out.reconciled_seqs // successfully reconciled
+    .map { barcode, seq ->
+        // drops the last part of the path (reconciled_seqs file) as trycycler
+        // searches the parent dir for it
+        Path cluster_dir = seq.getParent()
+        return [barcode, cluster_dir] 
+    }
+  
+  // TRYCYCLER: Align
+  trycycler_msa(reconciled_cluster_dirs)
+
+  // TRYCYCLER: Partitioning reads
+  clusters_to_partition =
+    trycycler_msa.out.results_dir
+    .groupTuple()
+    .join(porechop.out.trimmed_fq)
+
+  trycycler_partition(clusters_to_partition)
+
+  // TRYCYCLER: Generate consensus assemblies  
+  clusters_for_consensus =
+    trycycler_partition.out.partitioned_reads
+    .transpose() // "ungroup" tuple
+    .map { barcode, reads ->
+        // Get directories of successfully partitioned reads
+        Path cluster_dir = reads.getParent()
+        return [barcode, cluster_dir]
+    }
 
-  medaka_polish_flye(flye_polish_in)
-
-  // QUAST QC FLYE-ONLY ASSEMBLY 
-  quast_qc_flye_chromosomes(medaka_polish_flye.out.flye_polished)
-
-  // BAKTA ANNOTATE FLYE-ONLY CHROMOSOME FEATURES 
-  bakta_annotation_flye_chromosomes(medaka_polish_flye.out.flye_polished,get_bakta.out.bakta_db)
-
-  // BUSCO ANNOTATE FLYE-ONLY-CHROMOSOME FEATURES
-  busco_annotation_flye_chromosomes(bakta_annotation_flye_chromosomes.out.bakta_annotations, get_busco.out.busco_db)
-
-  // AMRFINDERPLUS ANNOTATE FLYE-ONLY AMR-GENES
-  amrfinderplus_annotation_flye_chromosomes(bakta_annotation_flye_chromosomes.out.bakta_annotations,
-                                            get_amrfinderplus.out.amrfinderplus_db)
+  trycycler_consensus(clusters_for_consensus)
 
-  flye_only_processed_samples=amrfinderplus_annotation_flye_chromosomes.out
-                              .map { it[0] }.collect()
+  // MEDAKA: Polish consensus assembly
+  consensus_dir = 
+    // Get parent dir for assembly
+    trycycler_consensus.out.cluster_assembly
+    .map { barcode, assembly ->
+        Path assembly_dir = assembly.getParent()
+        return [barcode, assembly_dir]
+    }
 
-  // ABRICATE ANNOTATE FLYE-CHROMOSOME WITH VFDB-GENES
-  abricateVFDB_annotation_flye_chromosomes(medaka_polish_flye.out.flye_polished)
+  medaka_polish_consensus(consensus_dir)
+
+  // CAT: Combine polished clusters consensus assemblies into a single fasta
+  polished_clusters = 
+    medaka_polish_consensus.out.cluster_assembly
+    .groupTuple()
+    .map { barcode, fastas ->
+        // Need to avoid filename collisions with consensus.fasta files
+        // by renaming them
+        def indexed_fas = 
+            fastas.withIndex()
+            .collect { fa, idx ->
+                def new_fa = fa.getParent() / "consensus_${idx}.fasta"
+                fa.copyTo(new_fa)
+                return new_fa
+            }
+        return [barcode, indexed_fas]
+    }
   
-  kraken_input_to_create_phylogeny_tree = kraken2.out
-                                            .map { [it[1]] }
-	                                          .collect()
-
-  consensus_bakta=bakta_annotation_chromosomes.out.bakta_annotations
-                  .map { [it[1]] }.collect()
+  concat_fastas(polished_clusters)
+
+  polished_consensus_per_barcode = concat_fastas.out
+
+  // MEDAKA: POLISH DE NOVO ASSEMBLIES
+  unpolished_denovo_assemblies =
+    unicycler_assembly.out.unicycler_assembly
+    .mix(flye_assembly.out.flye_assembly)
+    .map { barcode, assembly_dir -> 
+        // Get the assembler name by parsing the publishDir path.
+        // A better way to do this is output i.e. val(assembler_name) in the
+        // assembly processes but will required more changes
+        String assembler_name = assembly_dir.toString().tokenize("_")[-2]
+        return [barcode, assembler_name, assembly_dir] 
+    }
+    .combine(porechop.out.trimmed_fq, by: 0)
+
+  medaka_polish_denovo(unpolished_denovo_assemblies)
+
+  // ASSEMBLY QC
+  all_polished =
+    polished_consensus_per_barcode
+    .map { barcode, consensus_fa ->
+        // technically should be "trycycler" but want to separate it out from
+        // the denovo assemblies clearly
+        String assembler = "consensus"
+        return [barcode, assembler, consensus_fa]
+    }
+    .mix(medaka_polish_denovo.out.assembly)
 
-  flye_only_bakta=bakta_annotation_flye_chromosomes.out.bakta_annotations
-                  .map { [it[1]] }.collect()
+  // TODO: probably better to collect all per-barcode assemblies in one quast
+  // run to void a parsing/merging step
+  quast_qc_chromosomes(all_polished)
+  busco_qc_chromosomes(all_polished, get_busco.out.busco_db)
+  
+  // SELECT "BEST" ASSEMBLY
+  // TODO: Discuss better approaches. Currently selects the best assembly per
+  // barcode by most Complete BUSCO % 
+  barcode_busco_jsons =
+    // Gather all jsons for each barcode
+    busco_qc_chromosomes.out.json_summary
+    .groupTuple()
+
+  select_assembly(barcode_busco_jsons)
+  
+  best_chr_assembly = 
+    select_assembly.out
+    .map { barcode, txt ->
+      // best assembly stored in txt file for pipeline caching
+      String best = txt.splitText()[0].strip()
+      return [barcode, best]
+    }
+    .join(all_polished, by: [0, 1])
+
+  // ANNOTATE THE BEST CHROMOSOMAL ASSEMBLY PER-BARCODE
+  // BAKTA: Annotate gene features
+  bakta_annotation_chromosomes(best_chr_assembly, get_bakta.out.bakta_db)
+
+  // ABRICATE: Annotate VFDB genes
+  abricateVFDB_annotation_chromosomes(best_chr_assembly)
+
+  // AMRFINDERPLUS: Annotate AMR genes
+  amrfinderplus_annotation_chromosomes(
+    bakta_annotation_chromosomes.out.faa,
+    get_amrfinderplus.out.amrfinderplus_db
+  )
+
+  // CREATE FILES FOR PHYLOGENETIC TREE BUILDING
+  // Collect all the output (annotation) reports required for tree building
+  kraken2_reports =
+    // Collect all k2 reports and drop barcodes
+    kraken2.out
+    .map { barcode, k2_report -> k2_report }
+    .collect()
 
-// CREATE FILES FOR PHYLOGENETIC TREE BUILDING
-// Check if flye_only_bakta is empty, and use only consensus_bakta if it is
-all_bakta_input_to_create_phylogeny_tree = flye_only_bakta
-    .ifEmpty([]) // If flye_only_bakta is empty, provide an empty list
-    .merge(consensus_bakta) // Merge with consensus_bakta
-    //.view()
+  bakta_results_dirs = 
+    // TODO: Currently takes dir as input, amend the phylo building .py file
+    // to take direct inputs
+    bakta_annotation_chromosomes.out.txt
+    .map { barcode, assembler, txt -> 
+        Path dir = txt.getParent()
+        return dir
+    } 
+    .collect()
 
-create_phylogeny_tree_related_files(
+  create_phylogeny_tree_related_files(
     get_ncbi.out.assembly_summary_refseq,
-    kraken_input_to_create_phylogeny_tree,
-    all_bakta_input_to_create_phylogeny_tree
-)
-
-  // ORTHOFINDER PHYLOGENETIC ORTHOLOGY INFERENCE
-  run_orthofinder(create_phylogeny_tree_related_files.out.phylogeny_folder)
-
-
-  // AMRIFINDER ANNOTATE REFERENCE STRAINS FOR AMR GENES
-  amrfinderplus_annotation_reference(create_phylogeny_tree_related_files.out.phylogeny_folder,
-                                    get_amrfinderplus.out.amrfinderplus_db)
-
-  // ABRICATE ANNOTATE REFERENCE STRAINS FOR AMR GENES
-  abricateVFDB_annotation_reference(create_phylogeny_tree_related_files.out.phylogeny_folder) 
-
-  // GENERATE AMRFINDERPLUS gene matrix (FOR PHYLOGENY-AMR HEATMAP) 
-  consensus_amrfinderplus_output=amrfinderplus_annotation_chromosomes.out
-                                  .map { it[1] }
-                                  .collect()
-
-  flye_only_amrfinderplus_output=amrfinderplus_annotation_flye_chromosomes.out
-                                  .map { it[1] }
-                                  .collect()
-
-// Check if flye_only_amrfinderplus_output is empty, and use only consensus_amrfinderplus_output if it is
-  all_samples_amrfinderplus_output = flye_only_amrfinderplus_output
-    .ifEmpty([]) // If flye_only_amrfinderplus_output is empty, provide an empty list
-    .merge(consensus_amrfinderplus_output) // Merge with consensus_amrfinderplus_output
+    kraken2_reports,
+    bakta_results_dirs
+  )
+
+  // ORTHOFINDER: Infer phylogeny using orthologous genes
+  phylogeny_in = create_phylogeny_tree_related_files.out.phylogeny_folder
+  run_orthofinder(phylogeny_in)
+
+  // ANNOTATE REFERENCE STRAINS
+  // AMRFINDERPLUS: Annotate AMR genes
+  amrfinderplus_annotation_reference(
+    phylogeny_in,
+    get_amrfinderplus.out.amrfinderplus_db
+  )
+
+  // ABRICATE: Annotate VFDB genes
+  abricateVFDB_annotation_reference(phylogeny_in) 
+
+  // PYTHON: Generate gene matrix for phylogeny-AMR heatmap (AMRFINDERPLUS)
+  amrfinderplus_chr_reports =
+    amrfinderplus_annotation_chromosomes.out.report
+    .map { barcode, assembler, report -> report }
+    .collect()
 
-  all_references_amrfinderplus_output = amrfinderplus_annotation_reference.out.amrfinderplus_annotations
-  
   barcode_species_table = create_phylogeny_tree_related_files.out.barcode_species_table
 
-  generate_amrfinderplus_gene_matrix(all_samples_amrfinderplus_output,
-                                      all_references_amrfinderplus_output,
-                                      barcode_species_table)
-
-  // GENERATE ABRICATE-VFDB gene matrix (FOR PHYLOGENY-AMR HEATMAP)
-  consensus_abricate_output=abricateVFDB_annotation_chromosomes.out
-                            .map { it[1] }
-                            .collect()
-
-  flye_only_abricate_output=abricateVFDB_annotation_flye_chromosomes.out
-                            .map { it[1] }
-                            .collect()
-
-//  all_samples_abricate_output = consensus_abricate_output
-//                                .merge(flye_only_abricate_output)
+  generate_amrfinderplus_gene_matrix(
+    amrfinderplus_chr_reports,
+    amrfinderplus_annotation_reference.out.amrfinderplus_annotations,
+    barcode_species_table
+  )
 
-// Check if flye_only_abricate_output is empty, and use only consensus_abricate_output if it is
-all_samples_abricate_output = flye_only_abricate_output
-    .ifEmpty([]) // If flye_only_abricate_output is empty, provide an empty list
-    .merge(consensus_abricate_output) // Merge with consensus_abricate_output
-
-  all_references_abricate_output = abricateVFDB_annotation_reference.out.abricate_annotations
+  // PYTHON: Generate gene matrix for phylogeny-AMR heatmap (ABRICATE)
+  abricate_chr_reports = 
+    abricateVFDB_annotation_chromosomes.out.report
+    .map { barcode, report -> report }
+    .collect()
 
-  generate_abricate_gene_matrix(all_samples_abricate_output,
-                                all_references_abricate_output,
-                                barcode_species_table)
+  generate_abricate_gene_matrix(
+    abricate_chr_reports,
+    abricateVFDB_annotation_reference.out.abricate_annotations,
+    barcode_species_table
+  )
 
-  // CREATE PHYLOGENETIC TREE + HEATMAP IMAGE
-  create_phylogeny_And_Heatmap_image(run_orthofinder.out.phylogeny_tree,
-                                    generate_amrfinderplus_gene_matrix.out.amrfinderplus_gene_matrix,
-                                    generate_abricate_gene_matrix.out.abricate_gene_matrix)
+  // R: Plot phylogeny and heatmap
+  create_phylogeny_And_Heatmap_image(
+    run_orthofinder.out.phylogeny_tree,
+    generate_amrfinderplus_gene_matrix.out.amrfinderplus_gene_matrix,
+    generate_abricate_gene_matrix.out.abricate_gene_matrix
+  )
 
-  // ANNOTATE PLASMID FEATURES (BATKA)
+  // BAKTA: Annotate plasmid gene features
   bakta_annotation_plasmids(plassembler.out.plassembler_fasta, get_bakta.out.bakta_db)
 
   // SUMMARISE RUN WITH MULTIQC REPORT
@@ -497,53 +485,41 @@ all_samples_abricate_output = flye_only_abricate_output
   nanoplot_required_for_multiqc = nanoplot_summary.out.nanoplot_summary.ifEmpty([])
   pycoqc_required_for_multiqc = pycoqc_summary.out.pycoqc_json.ifEmpty([])
 
-kraken2_required_for_multiqc = kraken2.out.kraken2_screen
+  kraken2_required_for_multiqc = 
+    kraken2.out.kraken2_screen
     .map { it[1] }
     .collect()
     .ifEmpty([])
 
-quast_required_for_multiqc = quast_qc_chromosomes.out.quast_qc_multiqc
-    .map { it[1] }
+  quast_required_for_multiqc = 
+    quast_qc_chromosomes.out.tsv
+    .map { barcode, assembler, tsv -> tsv }
     .collect()
-    .merge(
-        quast_qc_flye_chromosomes.out.quast_qc_multiqc
-        .map { it[1] }
-        .collect()
-        .ifEmpty([])
-    )
-
-bakta_required_for_multiqc = bakta_annotation_chromosomes.out.bakta_annotations_multiqc
-    .map { it[1] }
+
+  bakta_required_for_multiqc =
+    bakta_annotation_chromosomes.out.txt
+    .map { barcode, assembler, txt -> txt }
     .collect()
-    .merge(
-        bakta_annotation_flye_chromosomes.out.bakta_annotations_multiqc
-        .map { it[1] }
-        .collect()
-        .ifEmpty([])
-    )
-
-busco_required_for_multiqc = busco_annotation_chromosomes.out.busco_annotations
-    .map { it[1] }
+
+  busco_required_for_multiqc =
+    busco_qc_chromosomes.out.txt_summary
+    .map { barcode, assembler, txt -> txt }
     .collect()
-    .merge(
-        busco_annotation_flye_chromosomes.out.busco_annotations
-        .map { it[1] }
-        .collect()
-        .ifEmpty([])
-    )
-
-bakta_plasmids_required_for_multiqc = bakta_annotation_plasmids.out.bakta_annotations
+
+  bakta_plasmids_required_for_multiqc = 
+    bakta_annotation_plasmids.out.bakta_annotations
     .map { it[1] }
     .collect()
     .ifEmpty([])
 
-phylogeny_heatmap_plot_required_for_multiqc = create_phylogeny_And_Heatmap_image.out.combined_plot_mqc
+  phylogeny_heatmap_plot_required_for_multiqc = 
+    create_phylogeny_And_Heatmap_image.out.combined_plot_mqc
     .ifEmpty([])
 
-multiqc_config = params.multiqc_config
+  multiqc_config = params.multiqc_config
 
-// Run MultiQC with the gathered inputs
-multiqc_report(
+  // Run MultiQC with the gathered inputs
+  multiqc_report(
     pycoqc_required_for_multiqc,
     nanoplot_required_for_multiqc,
     multiqc_config,
@@ -553,7 +529,7 @@ multiqc_report(
     bakta_plasmids_required_for_multiqc,
     busco_required_for_multiqc,
     phylogeny_heatmap_plot_required_for_multiqc
-)
+  )
 }
 
 // Print workflow execution summary 
diff --git a/modules/concat_fa.nf b/modules/concat_fa.nf
new file mode 100755
index 0000000..c98a9d0
--- /dev/null
+++ b/modules/concat_fa.nf
@@ -0,0 +1,14 @@
+process concat_fastas {
+    tag "${barcode}"
+
+    input:
+    tuple val(barcode), path(fasta_files)
+
+    output:
+    tuple val(barcode), path("${barcode}_combined.fasta")
+
+    script:
+    """
+    cat $fasta_files > ${barcode}_combined.fasta
+    """
+}
diff --git a/modules/create_phylogeny_And_Heatmap_image.nf b/modules/create_phylogeny_And_Heatmap_image.nf
index 611c4e5..6918615 100644
--- a/modules/create_phylogeny_And_Heatmap_image.nf
+++ b/modules/create_phylogeny_And_Heatmap_image.nf
@@ -1,7 +1,7 @@
 process create_phylogeny_And_Heatmap_image {
 	tag "PLOTTING PHYLOGENETIC TREE WITH AMR AND VIRULENCE GENES"
   container 'oras://community.wave.seqera.io/library/bioconductor-ggtree_r-ape_r-phytools_r-tidyverse:bd310f2405bed388'  
-  publishDir "${params.outdir}/taxonomy", mode: 'symlink'
+  publishDir "${params.outdir}/taxonomy", mode: 'copy'
   
   input:
   path(phylogeny_tree_base_path)
diff --git a/modules/create_phylogeny_tree_related_files.nf b/modules/create_phylogeny_tree_related_files.nf
index 632c0ad..e2b601c 100755
--- a/modules/create_phylogeny_tree_related_files.nf
+++ b/modules/create_phylogeny_tree_related_files.nf
@@ -1,16 +1,15 @@
 process create_phylogeny_tree_related_files {
-  tag "PREPARING INPUTS FOR PHYLOGENETIC TREE"  
   container 'python:3.8'
-  publishDir "${params.outdir}/taxonomy", mode: 'symlink'
+  publishDir "${params.outdir}/taxonomy", mode: 'copy'
   
   input:
   path(assembly_summary_refseq)
   path(kraken2_reports)
-	path(bakta_results)
+  path(bakta_results)
 
   output:
-	path("phylogeny"), emit: phylogeny_folder
-	path("barcode_species_table_mqc.txt"), emit: barcode_species_table
+  path("phylogeny"), emit: phylogeny_folder
+  path("barcode_species_table_mqc.txt"), emit: barcode_species_table
 
   script: 
   """
diff --git a/modules/generate_abricate_gene_matrix.nf b/modules/generate_abricate_gene_matrix.nf
index c328dd7..9b57a82 100755
--- a/modules/generate_abricate_gene_matrix.nf
+++ b/modules/generate_abricate_gene_matrix.nf
@@ -1,7 +1,7 @@
 process generate_abricate_gene_matrix {
   tag "GENERATING ABRICATE GENE MATRIX FOR ALL SAMPLES: ${params.input}"  
   container 'python:3.8'
-  publishDir "${params.outdir}/taxonomy", mode: 'symlink'
+  publishDir "${params.outdir}/taxonomy", mode: 'copy'
   
   input:
     path(abricate_output_all_samples)
diff --git a/modules/generate_amrfinderplus_gene_matrix.nf b/modules/generate_amrfinderplus_gene_matrix.nf
index 0c98cf1..e9f2d76 100755
--- a/modules/generate_amrfinderplus_gene_matrix.nf
+++ b/modules/generate_amrfinderplus_gene_matrix.nf
@@ -1,7 +1,7 @@
 process generate_amrfinderplus_gene_matrix {
   tag "GENERATING AMRFINDERPLUS GENE MATRIX FOR ALL SAMPLES: ${params.input}"  
   container 'python:3.8'
-  publishDir "${params.outdir}/taxonomy", mode: 'symlink'
+  publishDir "${params.outdir}/taxonomy", mode: 'copy'
   
   input:
   path(amrfinderplus_output_all_samples)
diff --git a/modules/run_abricateVFDB_annotation_chromosomes.nf b/modules/run_abricateVFDB_annotation_chromosomes.nf
index 59f225e..7ed04b9 100644
--- a/modules/run_abricateVFDB_annotation_chromosomes.nf
+++ b/modules/run_abricateVFDB_annotation_chromosomes.nf
@@ -1,26 +1,23 @@
 process abricateVFDB_annotation_chromosomes {
-  tag "ANNOTATING CONSENSUS ASSEMBLY WITH ABRICATE VFDB: ${barcode}"
+  tag "VFDB GENES: ${barcode}: ${assembler}"
   container 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_2'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
+  publishDir "${params.outdir}/annotations/${barcode}/abricate", mode: 'copy'
 
-input:
-  tuple val(barcode), path(medaka_consensus)
+  input:
+  tuple val(barcode), val(assembler), path(polished_fasta)
 
-output:
-  tuple val(barcode), path("abricate/*"), emit: abricate_annotations, optional: true 
+  output:
+  tuple val(barcode), path("*.txt"), emit: report
 
-script:
+  script:
+  prefix = "${barcode}_${assembler}_chr"
+  db_name = 'vfdb'
   """
-  for dir in ${medaka_consensus}; do  
-  	cat \${dir}/consensus.fasta >> concatenated_consensus.fasta
-  done
-
-  db_name='vfdb'
-  mkdir -p abricate
-
-  abricate concatenated_consensus.fasta \\
-	-db \${db_name} > abricate/${barcode}.txt
- 
+  abricate \\
+    $polished_fasta \\
+	-db ${db_name} \\
+    --threads $task.cpus \\
+    > ${prefix}.txt
   """
 
 }
diff --git a/modules/run_abricateVFDB_annotation_flye_chromosomes.nf b/modules/run_abricateVFDB_annotation_flye_chromosomes.nf
deleted file mode 100644
index e1ddc4d..0000000
--- a/modules/run_abricateVFDB_annotation_flye_chromosomes.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-process abricateVFDB_annotation_flye_chromosomes {
-   tag "ANNOTATING FLYE ASSEMBLY WITH ABRICATE VFDB: ${barcode}"
-   container 'quay.io/biocontainers/abricate:1.0.1--ha8f3691_2'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
-  
-input:
-  tuple val(barcode), path(medaka_flye)
-
-output:
-  tuple val(barcode), path("abricate/*"), emit: abricate_annotations, optional: true
-
-script:
-  """
-  db_name='vfdb'
-  mkdir -p abricate
-
-  abricate ${medaka_flye}/consensus.fasta \\
-     -db \${db_name} > abricate/${barcode}.txt  
-  """
-
-}
diff --git a/modules/run_amrfinderplus_annotation_chromosomes.nf b/modules/run_amrfinderplus_annotation_chromosomes.nf
index 06e62d6..9c96517 100644
--- a/modules/run_amrfinderplus_annotation_chromosomes.nf
+++ b/modules/run_amrfinderplus_annotation_chromosomes.nf
@@ -1,22 +1,22 @@
 process amrfinderplus_annotation_chromosomes {
-  tag "DETECTING AMR GENES: ${barcode}"
+  tag "${barcode}: ${assembler}"
   container 'quay.io/biocontainers/ncbi-amrfinderplus:3.12.8--h283d18e_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
+  publishDir "${params.outdir}/annotations/${barcode}/amrfinderplus", mode: 'copy'
   
-input:
-  tuple val(barcode), path(bakta_annotations)
+  input:
+  tuple val(barcode), val(assembler), path(annotated_faa)
   path(amrfinderplus_db)
 
-output:
-  tuple val(barcode), path("amrfinderplus/*"), emit: amrfinderplus_annotations
+  output:
+  tuple val(barcode), val(assembler), path("${prefix}.tsv"), emit: report
 
-script:
+  script:
+  prefix = "${barcode}_${assembler}_chr"
   """
-  mkdir -p amrfinderplus
-
-  amrfinder -p ${barcode}_bakta/${barcode}_chr.faa \\
-    -d ${amrfinderplus_db}/latest > amrfinderplus/${barcode}.txt
-
+  amrfinder \\
+    -p $annotated_faa \\
+    -d ${amrfinderplus_db}/latest \\
+    --threads $task.cpus > ${prefix}.tsv
   """
 
 }
diff --git a/modules/run_amrfinderplus_annotation_flye_chromosomes.nf b/modules/run_amrfinderplus_annotation_flye_chromosomes.nf
deleted file mode 100644
index 04bb4b9..0000000
--- a/modules/run_amrfinderplus_annotation_flye_chromosomes.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-process amrfinderplus_annotation_flye_chromosomes {
-  tag "DETECTING AMR GENES: ${barcode}"
-  container 'quay.io/biocontainers/ncbi-amrfinderplus:3.12.8--h283d18e_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
-  
-input:
-  tuple val(barcode), path(bakta_annotations)
-  path(amrfinderplus_db)
-
-output:
-  tuple val(barcode), path("amrfinderplus/*"), emit: amrfinderplus_annotations, optional: true
-
-script:
-  """
-  mkdir -p amrfinderplus
-
-  amrfinder -p ${barcode}_bakta/${barcode}_chr.faa \\
-    -d ${amrfinderplus_db}/latest > amrfinderplus/${barcode}.txt
-
-  """
-
-}
diff --git a/modules/run_bakta_annotation_chromosomes.nf b/modules/run_bakta_annotation_chromosomes.nf
index f89d9ff..1b7a077 100644
--- a/modules/run_bakta_annotation_chromosomes.nf
+++ b/modules/run_bakta_annotation_chromosomes.nf
@@ -1,29 +1,24 @@
 process bakta_annotation_chromosomes {
-  tag "ANNOTATING CONSENSUS ASSEMBLY WITH BATKA: ${barcode}"
+  tag "GENE FEATURES: ${barcode}: ${assembler}"
   container 'quay.io/biocontainers/bakta:1.9.2--pyhdfd78af_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
+  publishDir "${params.outdir}/annotations/${barcode}/bakta", mode: 'copy'
 
-input:
-  tuple val(barcode), path(medaka_consensus)
+  input:
+  tuple val(barcode), val(assembler), path(polished_fasta)
   path(bakta_db)
 
-output:
-  tuple val(barcode), path("${barcode}_bakta"), emit: bakta_annotations
-  tuple val(barcode), path("${barcode}_bakta/${barcode}_chr.txt"), emit: bakta_annotations_multiqc
+  output:
+  tuple val(barcode), val(assembler), path("${prefix}.faa"), emit: faa
+  tuple val(barcode), val(assembler), path("${prefix}.txt"), emit: txt
 
-script:
+  script:
+  prefix = "${barcode}_${assembler}_chr"
   """
-  for dir in ${medaka_consensus}; do  
-  	cat \${dir}/consensus.fasta >> concatenated_consensus.fasta
-  done
-
   bakta \\
-    concatenated_consensus.fasta \\
-    --db ${bakta_db} \\
-    --output ${barcode}_bakta \\
-    --prefix ${barcode}_chr \\
+    $polished_fasta \\
+    --db $bakta_db \\
+    --prefix $prefix \\
     --force \\
     --threads ${task.cpus}
-   
   """
 }
diff --git a/modules/run_bakta_annotation_flye_chromosomes.nf b/modules/run_bakta_annotation_flye_chromosomes.nf
deleted file mode 100644
index a760063..0000000
--- a/modules/run_bakta_annotation_flye_chromosomes.nf
+++ /dev/null
@@ -1,25 +0,0 @@
-process bakta_annotation_flye_chromosomes {
-  tag "ANNOTATING CONSENSUS ASSEMBLY WITH BATKA: ${barcode}"
-  container 'quay.io/biocontainers/bakta:1.9.2--pyhdfd78af_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
-
-input:
-  tuple val(barcode), path(medaka_flye)
-  path(bakta_db)
-
-output:
-  tuple val(barcode), path("${barcode}_bakta"), emit: bakta_annotations    
-  tuple val(barcode), path("${barcode}_bakta/${barcode}_chr.txt"), emit: bakta_annotations_multiqc
-
-script:
-  """
-  bakta \\
-    ${medaka_flye}/consensus.fasta \\
-    --db ${bakta_db} \\
-    --output ${barcode}_bakta \\
-    --prefix ${barcode}_chr \\
-    --force \\
-    --threads ${task.cpus}
-  """
-
-}
diff --git a/modules/run_bakta_annotation_plasmids.nf b/modules/run_bakta_annotation_plasmids.nf
index dc6b283..6fcafb5 100644
--- a/modules/run_bakta_annotation_plasmids.nf
+++ b/modules/run_bakta_annotation_plasmids.nf
@@ -1,7 +1,7 @@
 process bakta_annotation_plasmids {
   tag "ANNOTATING PLASMIDS: ${barcode}"
   container 'quay.io/biocontainers/bakta:1.9.2--pyhdfd78af_0'
-  publishDir "${params.outdir}/annotations/${barcode}/plasmids", mode: 'symlink'
+  publishDir "${params.outdir}/annotations/${barcode}/plasmids", mode: 'copy'
   
 input:
   tuple val(barcode), path(plassembler_plasmids)
diff --git a/modules/run_busco_annotation_chromosomes.nf b/modules/run_busco_annotation_chromosomes.nf
deleted file mode 100644
index aa07300..0000000
--- a/modules/run_busco_annotation_chromosomes.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-process busco_annotation_chromosomes {
-  tag "EVALUATING GENOME COMPLETENESS: ${barcode}"
-  container 'quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
-  
-input:
-  tuple val(barcode), path(bakta_annotations)
-  path(busco_db)
-  
-output:
-  tuple val(barcode), path("${barcode}_busco/short_summary.specific.*.txt"), emit: busco_annotations
-
-script:
-  """
-  busco \\
-    -f -i ${bakta_annotations}/${barcode}_chr.faa \\
-    -m proteins \\
-    --lineage_dataset busco_downloads/lineages/bacteria_odb10 \\
-    --out ${barcode}_busco --offline
-  """
-}
diff --git a/modules/run_busco_annotation_flye_chromosomes.nf b/modules/run_busco_annotation_flye_chromosomes.nf
deleted file mode 100644
index 316378b..0000000
--- a/modules/run_busco_annotation_flye_chromosomes.nf
+++ /dev/null
@@ -1,21 +0,0 @@
-process busco_annotation_flye_chromosomes {
-  tag "EVALUATING GENOME COMPLETENESS: ${barcode}"
-  container 'quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0'
-  publishDir "${params.outdir}/annotations/${barcode}", mode: 'symlink'
-
-input:
-  tuple val(barcode), path(bakta_annotations)
-  path(busco_db)
-
-output:
-  tuple val(barcode), path("${barcode}_busco/short_summary.specific.*.txt"), emit: busco_annotations
-
-script:
-  """
-  busco \\
-    -f -i ${bakta_annotations}/${barcode}_chr.faa \\
-    -m proteins --lineage_dataset busco_downloads/lineages/bacteria_odb10 \\
-    --out ${barcode}_busco --offline
-  """
-
-}
diff --git a/modules/run_busco_annotation_plasmids.nf b/modules/run_busco_annotation_plasmids.nf
index 926a04a..b215850 100644
--- a/modules/run_busco_annotation_plasmids.nf
+++ b/modules/run_busco_annotation_plasmids.nf
@@ -1,7 +1,7 @@
 process busco_annotation_plasmids {
   tag "EVALUATING PLASMID COMPLETENESS: ${barcode}"
   container 'quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0'
-  publishDir "${params.outdir}/assemblies/${barcode}/plasmids", mode: 'symlink'
+  publishDir "${params.outdir}/assemblies/${barcode}/plasmids", mode: 'copy'
 
 input:
   tuple val(barcode), path(bakta_annotations)
diff --git a/modules/run_busco_qc_chromosomes.nf b/modules/run_busco_qc_chromosomes.nf
new file mode 100644
index 0000000..d3c5703
--- /dev/null
+++ b/modules/run_busco_qc_chromosomes.nf
@@ -0,0 +1,27 @@
+process busco_qc_chromosomes {
+  tag "EVALUATING GENOME COMPLETENESS: ${barcode}: ${assembler}"
+  container 'quay.io/biocontainers/busco:5.6.1--pyhdfd78af_0'
+  publishDir "${params.outdir}/quality_control/${barcode}", mode: 'copy'
+  
+  input:
+  tuple val(barcode), val(assembler), path(polished_assembly)
+  path(busco_db)
+  
+  output:
+  tuple val(barcode), val(assembler), path("${prefix}"), emit: results
+  tuple val(barcode), val(assembler), path("${prefix}/short_summary.*.txt"), emit: txt_summary
+  tuple val(barcode), path("${prefix}/short_summary.*.json"), emit: json_summary
+
+  script:
+  prefix = "${barcode}_${assembler}_busco"
+  """
+  busco \\
+    --cpu $task.cpus \\
+    --in $polished_assembly \\
+    --out ${prefix} \\
+    --mode genome \\
+    --lineage_dataset busco_downloads/lineages/bacteria_odb10 \\
+    --force \\
+    --offline
+  """
+}
diff --git a/modules/run_kraken2.nf b/modules/run_kraken2.nf
index 48bcf11..a805de7 100755
--- a/modules/run_kraken2.nf
+++ b/modules/run_kraken2.nf
@@ -1,7 +1,7 @@
 process kraken2 {
   tag "DETECTING POSSIBLE CONTAMINATION: ${barcode}"
   container 'quay.io/biocontainers/kraken2:2.1.3--pl5321hdcf5f25_0'
-  publishDir "${params.outdir}/quality_control/${barcode}_kraken2", mode: 'symlink'
+  publishDir "${params.outdir}/quality_control/${barcode}_kraken2", mode: 'copy'
 
   input:
   tuple val(barcode), path(trimmed_fq)
diff --git a/modules/run_medaka_polish_consensus.nf b/modules/run_medaka_polish_consensus.nf
index 2ec72d5..99dbb16 100644
--- a/modules/run_medaka_polish_consensus.nf
+++ b/modules/run_medaka_polish_consensus.nf
@@ -1,20 +1,20 @@
 process medaka_polish_consensus {
-  tag "POLISHING CONSENSUS ASSEMBLY: ${barcode}"
+  tag "${barcode}: ${cluster_dir}"
   container 'quay.io/biocontainers/medaka:1.11.3--py39h05d5c5e_0'
-  publishDir "${params.outdir}/assemblies/${barcode}_consensus", mode: 'symlink'
+  publishDir "${params.outdir}/assemblies/${barcode}_consensus", mode: 'copy'
 
   input:
-  tuple val(barcode), val(cluster_id), path(consensus_partition), path(consensus_consensus)  
+  tuple val(barcode), path(cluster_dir)
 
   output:
-  tuple val(barcode), val(cluster_id), path("${cluster_id}_polished"), emit: consensus_polished, optional: true
+  tuple val(barcode), path("consensus.fasta"), emit: cluster_assembly
 
   script:
   """
   medaka_consensus \\
-		-i ${consensus_partition}/4_reads.fastq \\
-		-d ${consensus_consensus}/7_final_consensus.fasta \\
-		-o ${cluster_id}_polished \\
-		-t ${task.cpus}
+    -i ${cluster_dir}/4_reads.fastq \\
+    -d ${cluster_dir}/7_final_consensus.fasta \\
+    -o ./ \\
+    -t ${task.cpus}
   """
 }
diff --git a/modules/run_medaka_polish_denovo.nf b/modules/run_medaka_polish_denovo.nf
new file mode 100644
index 0000000..aa4720b
--- /dev/null
+++ b/modules/run_medaka_polish_denovo.nf
@@ -0,0 +1,21 @@
+process medaka_polish_denovo {
+  tag "${assembler_name}: ${barcode}"
+  container 'quay.io/biocontainers/medaka:1.11.3--py39h05d5c5e_0'
+  publishDir "${params.outdir}/assemblies/${barcode}_${assembler_name}", mode: 'copy'
+
+  input:
+  tuple val(barcode), val(assembler_name), path(assembly), path(trimmed_fq)
+
+  output:
+  tuple val(barcode), val(assembler_name), path("consensus.fasta"), emit: assembly
+
+  script:
+  """
+  # ideally the assembly file is passed in directly
+  medaka_consensus \\
+    -i ${trimmed_fq} \\
+    -d ${assembly}/assembly.fasta \\
+    -o ./ \\
+    -t ${task.cpus}
+  """
+}
diff --git a/modules/run_medaka_polish_flye.nf b/modules/run_medaka_polish_flye.nf
deleted file mode 100644
index ff20401..0000000
--- a/modules/run_medaka_polish_flye.nf
+++ /dev/null
@@ -1,20 +0,0 @@
-process medaka_polish_flye {
-  tag "POLISHING FLYE ASSEMBLY: ${barcode}"
-  container 'quay.io/biocontainers/medaka:1.11.3--py39h05d5c5e_0'
-  publishDir "${params.outdir}/assemblies/${barcode}_flye", mode: 'symlink'
-
-  input:
-  tuple val(barcode), path(flye_assembly), path(trimmed_fq)
-
-  output:
-  tuple val(barcode), path("*"), emit: flye_polished, optional: true
-
-  script:
-  """
-  medaka_consensus \\
-	 -i ${trimmed_fq} \\
-	 -d ${flye_assembly}/assembly.fasta \\
-	 -o ${barcode}_polished \\
-	 -t ${task.cpus}
-  """
-}
diff --git a/modules/run_multiqc.nf b/modules/run_multiqc.nf
index 0c27daf..7758018 100644
--- a/modules/run_multiqc.nf
+++ b/modules/run_multiqc.nf
@@ -1,7 +1,7 @@
 process multiqc_report {
   tag "GENERATING SUMMARY REPORT"
   container 'quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0'
-  publishDir "${params.outdir}/report", mode: 'symlink'
+  publishDir "${params.outdir}/report", mode: 'copy'
 
   input:
   path(pycoqc)
diff --git a/modules/run_nanoplot.nf b/modules/run_nanoplot.nf
index 8099498..ef2f179 100755
--- a/modules/run_nanoplot.nf
+++ b/modules/run_nanoplot.nf
@@ -1,7 +1,7 @@
 process nanoplot_summary {
   tag "SUMMARISING RAW OUTPUT FROM ONT RUN: ${sequencing_summary.fileName}"
   container 'quay.io/biocontainers/nanoplot:1.42.0--pyhdfd78af_0'
-  publishDir "${params.outdir}/quality_control", mode: 'symlink'
+  publishDir "${params.outdir}/quality_control", mode: 'copy'
   
   input:
   path(sequencing_summary)
diff --git a/modules/run_orthofinder.nf b/modules/run_orthofinder.nf
index a412368..3c4d9ce 100644
--- a/modules/run_orthofinder.nf
+++ b/modules/run_orthofinder.nf
@@ -1,5 +1,5 @@
 process run_orthofinder{
-  tag "RUN ORTHOFINDER to generate Phylogeny tree"
+  tag "GENERATE PHYLOGENY"
   container 'quay.io/biocontainers/orthofinder:2.5.5--hdfd78af_2'
 
 input:
diff --git a/modules/run_plassembler.nf b/modules/run_plassembler.nf
index 4e3ce3c..88e5e41 100644
--- a/modules/run_plassembler.nf
+++ b/modules/run_plassembler.nf
@@ -1,7 +1,7 @@
 process plassembler {
   tag "DETECTING PLASMIDS AND OTHER MOBILE ELEMENTS: ${barcode}"
   container 'quay.io/gbouras13/plassembler:1.6.2'
-  publishDir "${params.outdir}/assemblies", mode: 'symlink'
+  publishDir "${params.outdir}/assemblies", mode: 'copy'
 
   input:
   tuple val(barcode), path(trimmed_fq), path(flye_assembly)
diff --git a/modules/run_pycoqc.nf b/modules/run_pycoqc.nf
index 7405d0b..cd3308e 100755
--- a/modules/run_pycoqc.nf
+++ b/modules/run_pycoqc.nf
@@ -1,7 +1,7 @@
 process pycoqc_summary {
   tag "SUMMARISING RAW OUTPUT FROM ONT RUN: ${sequencing_summary.fileName}"
   container 'quay.io/biocontainers/pycoqc:2.5.2--py_0'
-  publishDir "${params.outdir}/quality_control", mode: 'symlink'
+  publishDir "${params.outdir}/quality_control", mode: 'copy'
 
   input:
   path(sequencing_summary)
diff --git a/modules/run_quast_qc_chromosomes.nf b/modules/run_quast_qc_chromosomes.nf
index d711638..62c2d2e 100644
--- a/modules/run_quast_qc_chromosomes.nf
+++ b/modules/run_quast_qc_chromosomes.nf
@@ -1,27 +1,25 @@
 process quast_qc_chromosomes {
-  tag "EVALUATING GENOME QUALITY: ${barcode}"
+  tag "EVALUATING GENOME QUALITY: ${barcode}: ${assembler}"
   container 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1'
-  publishDir "${params.outdir}/quality_control", mode: 'symlink'
+  publishDir "${params.outdir}/quality_control/${barcode}", mode: 'copy'
 
-input:
-  tuple val(barcode), path(medaka_consensus)
+  input:
+  tuple val(barcode), val(assembler), path(polished_assembly)
 
-output:
-  tuple val(barcode), path("${barcode}_quast"), emit: quast_qc
-  tuple val(barcode), path("${barcode}_quast/${barcode}.tsv"), emit: quast_qc_multiqc
+  output:
+  tuple val(barcode), val(assembler), path("${prefix}"), emit: results
+  tuple val(barcode), val(assembler), path("${prefix}.tsv"), emit: tsv
 
-script:
+  script:
+  prefix = "${barcode}_${assembler}"
   """
-  for dir in ${medaka_consensus}; do  
-  	cat \${dir}/consensus.fasta >> concatenated_consensus.fasta
-  done
-
   quast.py \\
-        --output-dir ${barcode}_quast \\
-        -l ${barcode} \\
-        concatenated_consensus.fasta
+    --output-dir $prefix \\
+    $polished_assembly \\
+    --threads $task.cpus
 
-  mv ${barcode}_quast/report.tsv ${barcode}_quast/${barcode}.tsv 
+  # multiqc requires tsv to be named with sample
+  ln -s ${prefix}/report.tsv ${prefix}.tsv
   """
 
 }
diff --git a/modules/run_quast_qc_flye_chromosomes.nf b/modules/run_quast_qc_flye_chromosomes.nf
deleted file mode 100644
index 1bb6c6a..0000000
--- a/modules/run_quast_qc_flye_chromosomes.nf
+++ /dev/null
@@ -1,24 +0,0 @@
-process quast_qc_flye_chromosomes {
-  tag "EVALUATING GENOME QUALITY: ${barcode}"
-  container 'quay.io/biocontainers/quast:5.2.0--py39pl5321h2add14b_1'
-  publishDir "${params.outdir}/quality_control", mode: 'symlink'
-
-input:
-  tuple val(barcode), path(medaka_flye)
-
-output:
-  tuple val(barcode), path("${barcode}_quast"), emit: quast_qc
-  tuple val(barcode), path("${barcode}_quast/${barcode}.tsv"), emit: quast_qc_multiqc
-
-script:
-  """
-
-  quast.py \\
-        --output-dir ${barcode}_quast \\
-        -l ${barcode} \\
-        ${medaka_flye}/consensus.fasta
-
-  mv ${barcode}_quast/report.tsv ${barcode}_quast/${barcode}.tsv 
-  """
-
-}
diff --git a/modules/run_trycycler_classify.nf b/modules/run_trycycler_classify.nf
index 573fff9..2214aff 100755
--- a/modules/run_trycycler_classify.nf
+++ b/modules/run_trycycler_classify.nf
@@ -6,12 +6,11 @@ process classify_trycycler {
   tuple val(barcode), path(trycycler_cluster), val(num_contigs)
 
   output:
-  tuple val(barcode), path("${barcode}_discarded/*"), emit: discard_contigs, optional: true
-  tuple val(barcode), path("${barcode}_for_reconciliation/*"), emit: reconcile_contigs
+  tuple val(barcode), path("${barcode}_discarded/*"), emit: clusters_to_discard, optional: true
+  tuple val(barcode), path("${barcode}_for_reconciliation/*"), emit: clusters_to_reconcile
 
   script: 
   """
-  classify_trycycler_clusters.py \\
-    ${barcode} 
+  classify_trycycler_clusters.py ${barcode} 
   """
 }
diff --git a/modules/run_trycycler_cluster.nf b/modules/run_trycycler_cluster.nf
index 842e8dd..16ac675 100755
--- a/modules/run_trycycler_cluster.nf
+++ b/modules/run_trycycler_cluster.nf
@@ -2,21 +2,23 @@ process trycycler_cluster {
   tag "CLUSTERING CONTIGS: ${barcode}"
   container 'quay.io/biocontainers/trycycler:0.5.4--pyhdfd78af_0'
 
-  errorStrategy 'ignore' // Ignore the error status
+  // Contigs can be filtered out to be < 2 within the process and segfault
+  errorStrategy { task.exitStatus == 1 ? 'ignore' : 'terminate' } 
 
   input:
-  tuple val(barcode), path(unicycler_assembly), path(flye_assembly), path(trimmed_fq)
+  tuple val(barcode), path(unicycler_assembly), path(flye_assembly), path(trimmed_fq), val(num_contigs)
 
   output:
-  tuple val(barcode), path("*"), path("${barcode}_cluster/contigs.phylip"), emit: trycycler_cluster
+  tuple val(barcode), path("${barcode}_cluster/"), emit: clusters
+  tuple val(barcode), path("${barcode}_cluster/contigs.phylip"), emit: phylip
 
-  script: 
+  script:
   """
   trycycler cluster \\
-    --assemblies ${barcode}_unicycler_assembly/assembly.fasta ${barcode}_flye_assembly/assembly.fasta \\
-    --reads ${barcode}_trimmed.fastq.gz \\
+    --assemblies ${unicycler_assembly}/assembly.fasta ${flye_assembly}/assembly.fasta \\
+    --reads $trimmed_fq \\
     --out_dir ${barcode}_cluster \\
     --min_contig_len ${params.trycycler_min_contig_length} \\
-    --threads ${task.cpus}  || true
+    --threads ${task.cpus}
   """
 }
diff --git a/modules/run_trycycler_consensus.nf b/modules/run_trycycler_consensus.nf
index 15b66b7..4d57d44 100644
--- a/modules/run_trycycler_consensus.nf
+++ b/modules/run_trycycler_consensus.nf
@@ -1,38 +1,17 @@
 process trycycler_consensus {
-  tag "GENERATING CONSENSUS ASSEMBLY: ${barcode}"
+  tag "GENERATING CONSENSUS ASSEMBLY: ${barcode}: ${cluster_dir}"
   container 'quay.io/biocontainers/trycycler:0.5.4--pyhdfd78af_0'
 
   input:
-  tuple val(barcode), val(cluster_id), path(msa), path(twoseq_and_partition)
+  tuple val(barcode), path(cluster_dir)
 
   output:
-  tuple val(barcode), val("${cluster_id}"), path("consensus_out"), emit: consensus_consensus
-
+  tuple val(barcode), path("**/7_final_consensus.fasta"), emit: cluster_assembly
 
   script:
-
   """
-  # Make a faux input directory to meet trycycler's expectations
-  mkdir -p consensus_in
- 
-  # Capture path to 2_all_seqs.fasta
-  cp ${twoseq_and_partition}/2_all_seqs.fasta consensus_in/
-
-  # Capture path to 3_msa.fasta
-  cp ${msa}/3_msa.fasta consensus_in/
-
-  # Capture path to 4_reads.fastq
-  cp ${twoseq_and_partition}/4_reads.fastq consensus_in/
-	
-  # Run trycycler reconcile step 
   trycycler consensus \\
-	--cluster_dir consensus_in \\
-        --threads ${task.cpus}
-
-  # Save output to new directory
-  mkdir -p consensus_out
-  cp consensus_in/5_chunked_sequence.gfa consensus_out/5_chunked_sequence.gfa
-  cp consensus_in/6_initial_consensus.fasta consensus_out/6_initial_consensus.fasta
-  cp consensus_in/7_final_consensus.fasta consensus_out/7_final_consensus.fasta
+	--cluster_dir $cluster_dir \\
+    --threads ${task.cpus}
   """
 }
diff --git a/modules/run_trycycler_msa.nf b/modules/run_trycycler_msa.nf
index 4aba759..74bff0a 100644
--- a/modules/run_trycycler_msa.nf
+++ b/modules/run_trycycler_msa.nf
@@ -1,30 +1,18 @@
 process trycycler_msa {
-  tag "MULTI SEQUENCE ALIGNMENT FOR SUCCESSFUL TRYCYCLER ASSEMBLY: ${barcode}"
+  tag "ALIGNING RECONCILED TRYCYCLER SEQS: ${barcode}: ${cluster_dir}"
   container 'quay.io/biocontainers/trycycler:0.5.4--pyhdfd78af_0'
 
   input:
-  tuple val(barcode), path(consensus_file), path(reconciled_dir)	
-
-  //when:
-  //consensus_good.exists()
+  tuple val(barcode), path(cluster_dir)	
 
   output:
-  tuple val(barcode), val("${barcode}_${reconciled_dir}"), path("${barcode}_${reconciled_dir}_msa"), emit: three_msa
+  tuple val(barcode), path("${cluster_dir}/"), emit: results_dir
+  tuple val(barcode), path("${cluster_dir}/3_msa.fasta"), emit: aligned_seqs
 
   script:
   """
-  # Capture path to reconciled directory
-  #reconciled_dir=\$(ls -d */* | grep 'barcode01_final/cluster_[0-9]*_reconciled')
-  #echo \$reconciled_dir
-
-  # Run trycycler MSA step: https://github.com/rrwick/Trycycler/wiki/Multiple-sequence-alignment
   trycycler msa \\
-    --cluster_dir $reconciled_dir \\
+    --cluster_dir $cluster_dir \\
     --threads ${task.cpus}
-  
-  # Move the 3_msa.fasta to out directory
-  mkdir -p ${barcode}_${reconciled_dir}_msa
-  cp ${reconciled_dir}/3_msa.fasta ${barcode}_${reconciled_dir}_msa/3_msa.fasta  
-
   """
 }
diff --git a/modules/run_trycycler_partition.nf b/modules/run_trycycler_partition.nf
index a1a2a78..be669a0 100644
--- a/modules/run_trycycler_partition.nf
+++ b/modules/run_trycycler_partition.nf
@@ -3,35 +3,17 @@ process trycycler_partition {
   container 'quay.io/biocontainers/trycycler:0.5.4--pyhdfd78af_0'
 
   input:
-  tuple val(barcode), path(consensus_file), path(consensus_good), path(trimmed_fq)
+  tuple val(barcode), path(cluster_dirs), path(trimmed_fq)
 
-  //when:
-  //consensus_good.exists()
-  
   output: 
-  tuple val(barcode), path("${barcode}_partitioned"), emit: four_reads
+  tuple val(barcode), path("**/4_reads.fastq"), emit: partitioned_reads
 
   script: 
   """ 
-  # Capture path to reconciled directory
-  reconciled_dir=\$(find -L . -type d -name 'cluster_*_reconciled')
-  echo \$reconciled_dir
-
-  echo $consensus_good
-
-  # Run trycycler partition step: https://github.com/rrwick/Trycycler/wiki/Partitioning-reads
   trycycler partition \\
-    --reads ${barcode}_trimmed.fastq.gz \\
-    --cluster_dirs \$reconciled_dir
-
-  # Move files to out directory
-  mkdir -p ${barcode}_partitioned
-  for dir in \$reconciled_dir; do
-    mkdir -p ${barcode}_partitioned/\${dir}
-    cp \${dir}/2_all_seqs.fasta ${barcode}_partitioned/\${dir}/2_all_seqs.fasta
-    cp \${dir}/4_reads.fastq ${barcode}_partitioned/\${dir}/4_reads.fastq
-  
-  done
+    --reads $trimmed_fq \\
+    --cluster_dirs $cluster_dirs \\
+    --threads ${task.cpus}
   """
 
 }
diff --git a/modules/run_trycycler_reconcile.nf b/modules/run_trycycler_reconcile.nf
index 0f7536d..7350d2d 100755
--- a/modules/run_trycycler_reconcile.nf
+++ b/modules/run_trycycler_reconcile.nf
@@ -1,35 +1,26 @@
 process trycycler_reconcile {
-  tag "RECONCILING CONTIGS: ${barcode}:${reconcile_contigs}"
+  tag "RECONCILING CONTIGS: ${barcode}: ${cluster_dir}"
   container 'quay.io/biocontainers/trycycler:0.5.4--pyhdfd78af_0'
 
   input:
-  tuple val(barcode), path(reconcile_contigs), path(trimmed_fq)
+  tuple val(barcode), path(cluster_dir), path(trimmed_fq)
 
   output: 
-  tuple val(barcode), path("${reconcile_contigs}_reconciled/"), emit: reconciled_seqs, optional: true
-   
+  tuple val(barcode), path("${cluster_dir}/"), emit: results_dir
+  tuple val(barcode), path("${cluster_dir}/2_all_seqs.fasta"), emit: reconciled_seqs, optional: true 
+  /* 
+   * optional:true as reconcililation may be unsuccessful (true negative) 
+   * i.e. if there is too much of a length difference between contigs in the 
+   * one cluster
+   */
+
   script: 
   """
-  echo "Running trycycler reconcile for barcode: ${barcode}"
-  echo "Input directory: ${reconcile_contigs}"
-  echo "Output directory: ${reconcile_contigs}_reconciled/"
-  echo "Trimmed reads: ${barcode}_trimmed.fastq.gz"
-
   trycycler reconcile \\
-      --reads ${barcode}_trimmed.fastq.gz \\
-      --cluster_dir ${reconcile_contigs} \\
+      --reads $trimmed_fq \\
+      --cluster_dir $cluster_dir \\
       --threads ${task.cpus} \\
       --min_1kbp_identity 10 \\
       --max_add_seq 2500
-
-  if [ -f "${reconcile_contigs}/2_all_seqs.fasta" ]; then
-        echo "File 2_all_seqs.fasta found, moving to output directory."
-        # Set up the output directory
-        mkdir -p ${reconcile_contigs}_reconciled/
-        # Move output from input directory to _reconciled output directory
-        mv ${reconcile_contigs}/2_all_seqs.fasta ${reconcile_contigs}_reconciled/2_all_seqs.fasta
-  else
-        echo "File 2_all_seqs.fasta not found. Please check the trycycler reconcile command and input files."
-  fi
   """
 }
diff --git a/modules/select_assembly.nf b/modules/select_assembly.nf
index e53e489..dbd2c5b 100755
--- a/modules/select_assembly.nf
+++ b/modules/select_assembly.nf
@@ -1,23 +1,17 @@
 process select_assembly {
-  tag "EVALUATING CONSENSUS ASSEMBLY QUALITY: ${barcode}"  
+  tag "${barcode}"  
   container 'python:3.8'
 
   input:
-  tuple val(barcode), path(reconciled), path(flye_assembly), path(kraken2_report)
-  path(ncbi_lookup)
+  tuple val(barcode), path(busco_jsons)
 
   output:
-  tuple val(barcode), path("Consensus.txt"), path("${barcode}_final/*"), emit: consensus_good, optional: true
-  tuple val(barcode), path("FlyeOnly.txt"), path("${barcode}_flye_assembly/Chr_contigs/"), emit: consensus_discard, optional: true
+  tuple val(barcode), path("best_assembly.txt")
 
   script: 
-  //TODO double check this is capturing all reconciled clusters
+  // Save to file (instead of print to stdout) for nextflow caching
   """
-  select_assembly.py \\
-    ${barcode} \\
-    ${reconciled.join(' ')} \\
-    ${flye_assembly} \\
-    ${kraken2_report} \\
-    ${ncbi_lookup}
+  compare_busco.py $busco_jsons > best_assembly.txt
   """
+  
 }
diff --git a/nextflow.config b/nextflow.config
index c613a75..4d3ed58 100755
--- a/nextflow.config
+++ b/nextflow.config
@@ -210,7 +210,7 @@ process {
     executor = 'pbspro'
     queue = 'normal'
     cpus = 1
-		time = '10h'
+	time = '10h'
     memory = 3.Gb
   }
 
@@ -238,12 +238,12 @@ process {
 		memory = 20.Gb
 	}
 
-	withName: 'medaka_polish_flye' {	
+	withName: 'medaka_polish_denovo' {	
 		executor = 'pbspro'
 		queue = 'normal'
 		cpus = 2 // medaka itself says more than 2 cpus is a waste
 		time = '10h'
-		memory = 40.Gb
+		memory = 20.Gb
 	}
 
 	withName: 'plassembler' {	
@@ -270,14 +270,6 @@ process {
     memory = 10.Gb
   }
 
-	withName: 'bakta_annotation_flye_chromosomes' {
-    executor = 'pbspro'
-    queue = 'normal'
-    cpus = 1
-    time = '10h'
-    memory = 10.Gb
-  }
-	
 	withName: 'quast_qc_chromosomes' {
     executor = 'pbspro'
     queue = 'normal'
@@ -286,14 +278,6 @@ process {
     memory = 5.Gb
   }
 
-	withName: 'quast_qc_flye_chromosomes' {
-    executor = 'pbspro'
-    queue = 'normal'
-    cpus = 1
-    time = '1h'
-    memory = 5.Gb
-  }
-
 	withName: 'abricateVFDB_annotation_chromosomes' {
     executor = 'pbspro'
     queue = 'normal'
@@ -302,14 +286,6 @@ process {
     memory = 2.Gb
   }
 
-	withName: 'abricateVFDB_annotation_flye_chromosomes' {
-    executor = 'pbspro'
-    queue = 'normal'
-   	cpus = 1
-    time = '1h'
-    memory = 2.Gb
-  }
-
 	withName: 'abricateVFDB_annotation_reference' {
     executor = 'pbspro'
     queue = 'normal'
@@ -326,14 +302,6 @@ process {
     memory = 2.Gb
   }
 
-	withName: 'amrfinderplus_annotation_flye_chromosomes' {
-    executor = 'pbspro'
-    queue = 'normal'
-    cpus = 1
-    time = '1h'
-    memory = 2.Gb
-  }
-
 	withName: 'amrfinderplus_annotation_reference' {
     executor = 'pbspro'
    	queue = 'normal'