diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1679a584..63376c9a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,10 +12,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#748](https://github.com/nf-core/mag/pull/748) - Fix broken phix reference channel when skipping phix removal (reported by @amizeranschi, fix by @muabnezor)
+- [#752](https://github.com/nf-core/mag/pull/752) - Fix QUAST results not being displayed when skipping certain steps (reported by @amizeranschi, fix by @jfy133)
 
 ### `Dependencies`
 
-### `Dependencies`
+### `Deprecated`
 
 ## 3.3.0 [2024-12-19]
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 5b76f018..5edd0881 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -18,7 +18,7 @@ data_format: "yaml"
 run_modules:
   - fastqc
   - fastp
-  - adapterRemoval
+  - adapterremoval
   - custom_content
   - bowtie2
   - busco
@@ -35,7 +35,7 @@ top_modules:
       path_filters_exclude:
         - "*trimmed*"
   - "fastp"
-  - "adapterRemoval"
+  - "adapterremoval"
   - "porechop"
   - "filtlong"
   - "fastqc":
@@ -118,12 +118,12 @@ custom_data:
 sp:
   host_removal:
     fn: "host_removal_metrics.tsv"
-  adapterRemoval:
+  adapterremoval:
     fn: "*_ar2.settings"
   kraken:
     fn_re: ".*[kraken2|centrifuge].*report.txt"
   quast:
-    fn_re: "report.*.tsv"
+    fn: "report*.tsv"
   filtlong:
     num_lines: 20
     fn_re: ".*_filtlong.log"
diff --git a/conf/modules.config b/conf/modules.config
index 701598db..e14432d6 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -28,20 +28,20 @@ process {
             "--cut_front",
             "--cut_tail",
             "--cut_mean_quality ${params.fastp_cut_mean_quality}",
-            "--length_required ${params.reads_minlength}"
+            "--length_required ${params.reads_minlength}",
         ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/QC_shortreads/fastp/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{html,json}"
+                pattern: "*.{html,json}",
             ],
             [
                 path: { "${params.outdir}/QC_shortreads/fastp/${meta.id}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz",
-                enabled: params.save_clipped_reads
-            ]
+                enabled: params.save_clipped_reads,
+            ],
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_fastp" }
         tag        = { "${meta.id}_run${meta.run}" }
@@ -52,20 +52,20 @@ process {
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1} --adapter2 ${params.adapterremoval_adapter2}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
-            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4"
+            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4",
         ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/QC_shortreads/adapterremoval/${meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{settings}"
+                pattern: "*.{settings}",
             ],
             [
                 path: { "${params.outdir}/QC_shortreads/adapterremoval/${meta.id}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{truncated,discarded}.gz",
-                enabled: params.save_clipped_reads
-            ]
+                enabled: params.save_clipped_reads,
+            ],
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
         tag        = { "${meta.id}_run${meta.run}" }
@@ -76,12 +76,12 @@ process {
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
-            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4"
+            params.adapterremoval_trim_quality_stretch ? "--trim_qualities" : "--trimwindows 4",
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/adapterremoval/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{settings}"
+            pattern: "*.{settings}",
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
         tag        = { "${meta.id}_run${meta.run}" }
@@ -93,14 +93,14 @@ process {
             [
                 path: { "${params.outdir}/QC_shortreads/remove_phix" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
             ],
             [
                 path: { "${params.outdir}/QC_shortreads/remove_phix" },
                 mode: params.publish_dir_mode,
                 pattern: "*.unmapped*.fastq.gz",
-                enabled: params.save_phixremoved_reads
-            ]
+                enabled: params.save_phixremoved_reads,
+            ],
         ]
         tag        = { "${meta.id}_run${meta.run}" }
     }
@@ -113,14 +113,14 @@ process {
             [
                 path: { "${params.outdir}/QC_shortreads/remove_host" },
                 mode: params.publish_dir_mode,
-                pattern: "*{.log,read_ids.txt}"
+                pattern: "*{.log,read_ids.txt}",
             ],
             [
                 path: { "${params.outdir}/QC_shortreads/remove_host" },
                 mode: params.publish_dir_mode,
                 pattern: "*.unmapped*.fastq.gz",
-                enabled: params.save_hostremoved_reads
-            ]
+                enabled: params.save_hostremoved_reads,
+            ],
         ]
         tag        = { "${meta.id}_run${meta.run}" }
     }
@@ -131,7 +131,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastqc" },
             mode: params.publish_dir_mode,
-            pattern: "*.html"
+            pattern: "*.html",
         ]
         tag        = { "${meta.id}_run${meta.run}" }
     }
@@ -139,22 +139,22 @@ process {
     withName: BBMAP_BBNORM {
         ext.args   = [
             params.bbnorm_target ? "target=${params.bbnorm_target}" : '',
-            params.bbnorm_min ? "min=${params.bbnorm_min}" : ''
+            params.bbnorm_min ? "min=${params.bbnorm_min}" : '',
         ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/bbmap/bbnorm/logs" },
                 enabled: params.save_bbnorm_reads,
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
             ],
             [
                 path: { "${params.outdir}/bbmap/bbnorm/" },
                 mode: 'copy',
                 enabled: params.save_bbnorm_reads,
                 mode: params.publish_dir_mode,
-                pattern: "*.fastq.gz"
-            ]
+                pattern: "*.fastq.gz",
+            ],
         ]
     }
 
@@ -163,7 +163,7 @@ process {
             path: { "${params.outdir}/QC_longreads/porechop" },
             mode: params.publish_dir_mode,
             pattern: "*_porechop_trimmed.fastq.gz",
-            enabled: params.save_porechop_reads
+            enabled: params.save_porechop_reads,
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_porechop_trimmed" }
     }
@@ -173,7 +173,7 @@ process {
             path: { "${params.outdir}/QC_longreads/porechop" },
             mode: params.publish_dir_mode,
             pattern: "*_porechop-abi_trimmed.fastq.gz",
-            enabled: params.save_porechop_reads
+            enabled: params.save_porechop_reads,
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_porechop-abi_trimmed" }
     }
@@ -184,13 +184,13 @@ process {
             "--keep_percent ${params.longreads_keep_percent}",
             "--trim",
             "--length_weight ${params.longreads_length_weight}",
-            params.longreads_min_quality ? "--min_mean_q ${params.longreads_min_quality}" : ''
+            params.longreads_min_quality ? "--min_mean_q ${params.longreads_min_quality}" : '',
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/QC_longreads/Filtlong" },
             mode: params.publish_dir_mode,
             pattern: "*_filtlong.fastq.gz",
-            enabled: params.save_filtered_longreads
+            enabled: params.save_filtered_longreads,
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_filtlong" }
     }
@@ -199,20 +199,20 @@ process {
         ext.args   = [
             "--min-len ${params.longreads_min_length}",
             params.longreads_min_quality ? "--min-qual ${params.longreads_min_quality}" : '',
-            "-vv"
+            "-vv",
         ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/QC_longreads/Nanoq" },
                 mode: params.publish_dir_mode,
                 pattern: "*_nanoq_filtered.fastq.gz",
-                enabled: params.save_filtered_longreads
+                enabled: params.save_filtered_longreads,
             ],
             [
                 path: { "${params.outdir}/QC_longreads/Nanoq" },
                 mode: params.publish_dir_mode,
-                pattern: "*_nanoq_filtered.stats"
-            ]
+                pattern: "*_nanoq_filtered.stats",
+            ],
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_nanoq_filtered" }
     }
@@ -222,14 +222,14 @@ process {
             [
                 path: { "${params.outdir}/QC_longreads/NanoLyse" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
             ],
             [
                 path: { "${params.outdir}/QC_longreads/NanoLyse" },
                 mode: params.publish_dir_mode,
                 pattern: "*_nanolyse.fastq.gz",
-                enabled: params.save_lambdaremoved_reads
-            ]
+                enabled: params.save_lambdaremoved_reads,
+            ],
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_lambdafiltered" }
     }
@@ -237,20 +237,20 @@ process {
     withName: CHOPPER {
         ext.args2  = [
             params.longreads_min_quality ? "--quality ${params.longreads_min_quality}" : '',
-            params.longreads_min_length ? "--minlength ${params.longreads_min_length}" : ''
+            params.longreads_min_length ? "--minlength ${params.longreads_min_length}" : '',
         ].join(' ').trim()
         publishDir = [
             [
                 path: { "${params.outdir}/QC_longreads/Chopper" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
             ],
             [
                 path: { "${params.outdir}/QC_longreads/Chopper" },
                 mode: params.publish_dir_mode,
                 pattern: "*_chopper.fastq.gz",
-                enabled: params.save_lambdaremoved_reads || params.save_filtered_longreads
-            ]
+                enabled: params.save_lambdaremoved_reads || params.save_filtered_longreads,
+            ],
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_chopper" }
     }
@@ -261,13 +261,13 @@ process {
             [
                 "-p raw_",
                 "--title ${meta.id}_raw",
-                "-c darkblue"
+                "-c darkblue",
             ].join(' ').trim()
         }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{png,html,txt}"
+            pattern: "*.{png,html,txt}",
         ]
     }
 
@@ -276,13 +276,13 @@ process {
             [
                 "-p filtered_",
                 "--title ${meta.id}_filtered",
-                "-c darkblue"
+                "-c darkblue",
             ].join(' ').trim()
         }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{png,html,txt}"
+            pattern: "*.{png,html,txt}",
         ]
     }
 
@@ -300,7 +300,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Taxonomy/kraken2/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.txt"
+            pattern: "*.txt",
         ]
     }
 
@@ -338,12 +338,12 @@ process {
         ext.args   = [
             "--cleanup",
             "--min-score ${params.genomad_min_score}",
-            "--splits ${params.genomad_splits}"
+            "--splits ${params.genomad_splits}",
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/VirusIdentification/geNomad/${meta.id}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -354,14 +354,14 @@ process {
             [
                 path: { "${params.outdir}/Assembly/${assembly_meta.assembler}/QC/${assembly_meta.id}" },
                 mode: params.publish_dir_mode,
-                pattern: "*.log"
+                pattern: "*.log",
             ],
             [
                 path: { "${params.outdir}/Assembly/${assembly_meta.assembler}/QC/${assembly_meta.id}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{bam,bai}",
-                enabled: params.save_assembly_mapped_reads
-            ]
+                enabled: params.save_assembly_mapped_reads,
+            ],
         ]
     }
 
@@ -373,7 +373,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning" },
             mode: params.publish_dir_mode,
-            pattern: "*.{png,tsv}"
+            pattern: "*.{png,tsv}",
         ]
     }
 
@@ -388,7 +388,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/BUSCO" },
             mode: params.publish_dir_mode,
-            pattern: "*.{log,err,faa.gz,fna.gz,gff,txt}"
+            pattern: "*.{log,err,faa.gz,fna.gz,gff,txt}",
         ]
     }
 
@@ -410,7 +410,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -420,7 +420,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -429,7 +429,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -439,7 +439,7 @@ process {
             mode: params.publish_dir_mode,
             overwrite: false,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_checkm2_data
+            enabled: params.save_checkm2_data,
         ]
     }
 
@@ -448,7 +448,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM2" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -457,7 +457,7 @@ process {
             path: { "${params.outdir}/GenomeBinning/QC/GUNC" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.gunc_save_db
+            enabled: params.gunc_save_db,
         ]
     }
 
@@ -466,7 +466,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${fasta.baseName}/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -475,7 +475,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${checkm_file.baseName}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 
@@ -496,13 +496,13 @@ process {
             "--extension fa",
             "--min_perc_aa ${params.gtdbtk_min_perc_aa}",
             "--min_af ${params.gtdbtk_min_af}",
-            "--pplacer_cpus ${params.gtdbtk_pplacer_cpus}"
+            "--pplacer_cpus ${params.gtdbtk_pplacer_cpus}",
         ].join(' ')
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/Taxonomy/GTDB-Tk/${meta.assembler}/${meta.binner}/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{log,tsv,tree.gz,fasta,fasta.gz}"
+            pattern: "*.{log,tsv,tree.gz,fasta,fasta.gz}",
         ]
     }
 
@@ -539,7 +539,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/variant_calling/consensus" },
             mode: params.publish_dir_mode,
-            pattern: "*.fa"
+            pattern: "*.fa",
         ]
     }
 
@@ -549,7 +549,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/variant_calling/index" },
             mode: params.publish_dir_mode,
-            enabled: false
+            enabled: false,
         ]
     }
 
@@ -557,7 +557,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
         ]
     }
 
@@ -566,7 +566,7 @@ process {
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
-            mode: params.publish_dir_mode
+            mode: params.publish_dir_mode,
         ]
     }
 
@@ -575,7 +575,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Ancient_DNA/samtools/faidx" },
             mode: params.publish_dir_mode,
-            enabled: false
+            enabled: false,
         ]
     }
 
@@ -590,7 +590,7 @@ process {
         ext.args   = [
             params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
             "--unbinned",
-            "--seed ${params.metabat_rng_seed}"
+            "--seed ${params.metabat_rng_seed}",
         ].join(' ').trim()
     }
 
@@ -599,13 +599,13 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/discarded" },
                 mode: params.publish_dir_mode,
-                pattern: '*.tooshort.gz'
+                pattern: '*.tooshort.gz',
             ],
             [
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/" },
                 mode: params.publish_dir_mode,
-                pattern: '*.{summary,abundance}'
-            ]
+                pattern: '*.{summary,abundance}',
+            ],
         ]
         ext.prefix = { "${meta.assembler}-MaxBin2-${meta.id}" }
     }
@@ -615,7 +615,7 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/bins/" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fa.gz'
+                pattern: '*.fa.gz',
             ]
         ]
     }
@@ -625,14 +625,14 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/CONCOCT/stats/" },
                 mode: params.publish_dir_mode,
-                pattern: "*.{txt,csv,tsv}"
+                pattern: "*.{txt,csv,tsv}",
             ],
             [
                 path: { "${params.outdir}/GenomeBinning/CONCOCT/bins" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> new File(filename).getName() },
-                pattern: "*/*.fa.gz"
-            ]
+                pattern: "*/*.fa.gz",
+            ],
         ]
         ext.prefix = { "${meta.assembler}-CONCOCT-${meta.id}" }
     }
@@ -662,7 +662,7 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/DASTool" },
                 mode: params.publish_dir_mode,
-                pattern: '*.{tsv,log,eval,seqlength}'
+                pattern: '*.{tsv,log,eval,seqlength}',
             ]
         ]
         ext.prefix = { "${meta.assembler}-DASTool-${meta.id}" }
@@ -674,13 +674,13 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/DASTool/unbinned" },
                 mode: params.publish_dir_mode,
-                pattern: '*-DASToolUnbinned-*.fa'
+                pattern: '*-DASToolUnbinned-*.fa',
             ],
             [
                 path: { "${params.outdir}/GenomeBinning/DASTool/bins" },
                 mode: params.publish_dir_mode,
-                pattern: '*-{MetaBAT2,MaxBin2,CONCOCT}Refined-*.fa'
-            ]
+                pattern: '*-{MetaBAT2,MaxBin2,CONCOCT}Refined-*.fa',
+            ],
         ]
     }
 
@@ -688,7 +688,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Taxonomy/Tiara/" },
             mode: params.publish_dir_mode,
-            pattern: "*.txt"
+            pattern: "*.txt",
         ]
         ext.args   = { "--min_len ${params.tiara_min_length} --probabilities" }
         ext.prefix = { "${meta.assembler}-${meta.id}.tiara" }
@@ -715,11 +715,11 @@ process {
         publishDir = [path: { "${params.outdir}/Annotation/MetaEuk/${meta.assembler}/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
     withName: MULTIQC {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
     }
 }