diff --git a/conf/modules.config b/conf/modules.config
index 747a03a..5127ff5 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -61,10 +61,17 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/fastp" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{log,html,json}'
+            ]
         ]
     }
 
@@ -82,10 +89,17 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/fastp" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{log,html,json}'
+            ]
         ]
     }
 
@@ -98,10 +112,17 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/adapterremoval" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/adapterremoval" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/adapterremoval" },
+                mode: params.publish_dir_mode,
+                pattern: '*.settings'
+            ]
         ]
     }
 
@@ -117,20 +138,34 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/adapterremoval" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/adapterremoval" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/adapterremoval" },
+                mode: params.publish_dir_mode,
+                pattern: '*.settings'
+            ]
         ]
     }
 
     withName: PORECHOP_PORECHOP {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/porechop" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq.gz',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/porechop" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/porechop" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ]
         ]
     }
 
@@ -143,10 +178,17 @@ process {
         .join(' ').trim()
         ext.prefix = { "${meta.id}_${meta.run_accession}_filtered" }
         publishDir = [
-            path: { "${params.outdir}/filtlong" },
-            mode: params.publish_dir_mode,
-            pattern: '*.{fastq.gz,log}',
-            enabled: params.save_preprocessed_reads
+            [
+                path: { "${params.outdir}/filtlong" },
+                mode: params.publish_dir_mode,
+                pattern: '*.fastq.gz',
+                enabled: params.save_preprocessed_reads
+            ],
+            [
+                path: { "${params.outdir}/filtlong" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ]
         ]
     }
 
@@ -163,21 +205,21 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}" }
         publishDir = [
             [
-            path: { "${params.outdir}/bowtie2/align" },
-            mode: params.publish_dir_mode,
-            pattern: '*.log'
+                path: { "${params.outdir}/bowtie2/align" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
             ],
             [
-            path: { "${params.outdir}/bowtie2/align" },
-            mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_mapped,
-            pattern: '*.bam'
+                path: { "${params.outdir}/bowtie2/align" },
+                mode: params.publish_dir_mode,
+                enabled: params.save_hostremoval_mapped,
+                pattern: '*.bam'
             ],
             [
-            path: { "${params.outdir}/bowtie2/align" },
-            mode: params.publish_dir_mode,
-            enabled: params.save_hostremoval_unmapped,
-            pattern: '*.fastq.gz'
+                path: { "${params.outdir}/bowtie2/align" },
+                mode: params.publish_dir_mode,
+                enabled: params.save_hostremoval_unmapped,
+                pattern: '*.fastq.gz'
             ]
         ]
     }
@@ -240,10 +282,17 @@ process {
             ].join(' ').trim()
         ext.prefix = { "${meta.id}-${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/bbduk/" },
-            mode: params.publish_dir_mode,
-            pattern: '*.{fastq.gz,log}',
-            enabled: params.save_complexityfiltered_reads
+            [
+                path: { "${params.outdir}/bbduk/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.{fastq.gz,log}',
+                enabled: params.save_complexityfiltered_reads
+            ],
+            [
+                path: { "${params.outdir}/bbduk/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ]
         ]
     }
 
@@ -255,10 +304,17 @@ process {
             ].join(' ').trim()
         ext.prefix = { "${meta.id}-${meta.run_accession}" }
         publishDir = [
-            path: { "${params.outdir}/prinseqplusplus/" },
-            mode: params.publish_dir_mode,
-            pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz,log}',
-            enabled: params.save_complexityfiltered_reads
+            [
+                path: { "${params.outdir}/prinseqplusplus/" },
+                mode: params.publish_dir_mode,
+                pattern: '*{_good_out.fastq.gz,_good_out_R1.fastq.gz,_good_out_R2.fastq.gz}',
+                enabled: params.save_complexityfiltered_reads
+            ],
+            [
+                path: { "${params.outdir}/prinseqplusplus/" },
+                mode: params.publish_dir_mode,
+                pattern: '*.log'
+            ]
         ]
     }
 
@@ -318,7 +374,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/bracken/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{txt}'
+            pattern: '*.txt'
         ]
     }