diff --git a/conf/modules.config b/conf/modules.config
index 747a03a..60ebaa4 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -33,7 +33,7 @@ process {
     }
 
     withName: FALCO {
-        ext.prefix = { "${meta.id}_${meta.run_accession}_raw" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}_raw_falco" }
         publishDir = [
             path: { "${params.outdir}/falco/raw" },
             mode: params.publish_dir_mode,
@@ -42,7 +42,7 @@ process {
     }
 
     withName: FALCO_PROCESSED {
-        ext.prefix = { "${meta.id}_${meta.run_accession}_processed" }
+        ext.prefix = { "${meta.id}_${meta.run_accession}_processed_falco" }
         publishDir = [
             path: { "${params.outdir}/falco/processed" },
             mode: params.publish_dir_mode,
@@ -61,10 +61,17 @@ process {
         ].join(' ').trim()
         ext.prefix = { "${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'
+            ]
         ]
     }
 
@@ -295,7 +351,7 @@ process {
 
     withName: KRAKEN2_KRAKEN2 {
         ext.args = params.kraken2_save_minimizers ? { "${meta.db_params} --report-minimizer-data" } : { "${meta.db_params}" }
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { meta.tool == "bracken" ? "${meta.id}-${meta.db_name}.bracken" : "${meta.id}-${meta.db_name}" } : { meta.tool == "bracken" ? "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" : "${meta.id}-${meta.run_accession}-${meta.db_name}" }
         publishDir = [
             path: { "${params.outdir}/kraken2/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -305,7 +361,7 @@ process {
 
     withName: BRACKEN_BRACKEN {
         errorStrategy = 'ignore'
-        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
+        ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}.bracken" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}.bracken" }
         publishDir = [
             path: { "${params.outdir}/bracken/${meta.db_name}/" },
             mode: params.publish_dir_mode,
@@ -318,7 +374,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/bracken/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{txt}'
+            pattern: '*.txt'
         ]
     }
 
diff --git a/modules.json b/modules.json
index a3017f7..7eb15e3 100644
--- a/modules.json
+++ b/modules.json
@@ -73,7 +73,8 @@
                     "falco": {
                         "branch": "master",
                         "git_sha": "fc959214036403ad83efe7a41d43d0606c445cda",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/falco/falco.diff"
                     },
                     "fastp": {
                         "branch": "master",
diff --git a/modules/nf-core/falco/falco.diff b/modules/nf-core/falco/falco.diff
new file mode 100644
index 0000000..4c726b9
--- /dev/null
+++ b/modules/nf-core/falco/falco.diff
@@ -0,0 +1,16 @@
+Changes in module 'nf-core/falco'
+--- modules/nf-core/falco/main.nf
++++ modules/nf-core/falco/main.nf
+@@ -33,7 +33,9 @@
+         """
+     } else {
+         """
+-        falco $args --threads $task.cpus ${reads}
++        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
++        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
++        falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
+ 
+         cat <<-END_VERSIONS > versions.yml
+         "${task.process}":
+
+************************************************************
diff --git a/modules/nf-core/falco/main.nf b/modules/nf-core/falco/main.nf
index 1688162..b279c57 100644
--- a/modules/nf-core/falco/main.nf
+++ b/modules/nf-core/falco/main.nf
@@ -33,7 +33,9 @@ process FALCO {
         """
     } else {
         """
-        falco $args --threads $task.cpus ${reads}
+        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
+        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
+        falco $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":