diff --git a/CHANGELOG.md b/CHANGELOG.md
index 75b6e128..be1d0138 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.3.0 - 2024-01-25 - Gray Zinc Dalmatian
 
+- [[#307]](https://github.com/nf-core/smrnaseq/pull/307) - Clean up config file and improve output folder structure
 - [[#299]](https://github.com/nf-core/smrnaseq/issues/299) - Bugfix for missing inputs in BAM stats (`genome_quant.r`)
 - [[#164]](https://github.com/nf-core/smrnaseq/pull/164) - UMI Handling Feature implemented in the pipeline
 - [[#302]](https://github.com/nf-core/smrnaseq/pull/302) - Merged in nf-core template v2.11.1
diff --git a/conf/modules.config b/conf/modules.config
index 127e0a34..b57e4f92 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -10,17 +10,22 @@
 ----------------------------------------------------------------------------------------
 */
 
-//
-// General configuration options
-//
+
 
 process {
+
+    //
+    // General configuration options
+    //
     publishDir = [
         path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
         mode: params.publish_dir_mode,
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    //
+    // Input preparation
+    //
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -28,327 +33,342 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
-    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
+    withName: 'CAT_FASTQ' {
         publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
+            path: { "${params.outdir}/cat_fastq" },
             mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
+            pattern: '*.fastq',
+            // enabled: params.save_merged_fastq //TODO ? implement save_merged_fastq param
         ]
     }
-}
-
-//
-// Genome preparation options
-//
 
-process {
-    withName: 'CAT_FASTQ' {
+    //
+    // FASTQ_FASTQC_UMITOOLS_FASTP
+    //
+    withName: '.*:FASTQC_UMITOOLS_FASTP:FASTP' {
+        ext.args = [ "",
+            params.trim_fastq              ? "" : "--disable_adapter_trimming",
+            params.clip_r1 > 0             ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
+            params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
+            params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
+            params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
+            params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}"
+        ].join(" ").trim()
         publishDir = [
-            path: { "${params.outdir}/fastq" },
-            mode: params.publish_dir_mode,
-            pattern: '*.fastq',
-            // enabled: params.save_merged_fastq //TODO ? implement save_merged_fastq param
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{json,html}"
+            ],
+            [
+                path: { "${params.outdir}/fastp/log" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/fastp" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fail.fastq.gz",
+                enabled: params.save_trimmed_fail
+            ]
         ]
     }
-    withName: 'INDEX_GENOME' {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
+        ext.args = '--quiet'
         publishDir = [
-            path: { "${params.outdir}/index" },
+            path: { "${params.outdir}/fastqc/raw" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_.*' {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
+        ext.args = '--quiet'
         publishDir = [
-            path: { "${params.outdir}/genome" },
+            path: { "${params.outdir}/fastqc/trimmed" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'EDGER_QC' {
+    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:UMITOOLS_EXTRACT' {
+        ext.args  = [
+            params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
+            params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
+        ].join(' ').trim()
         publishDir = [
-            path: { "${params.outdir}/edger" },
-            mode: params.publish_dir_mode,
-            enabled: true
+            [
+                path: { "${params.outdir}/umi_dedup/fastq_extracted_umi" },
+                mode: params.publish_dir_mode,
+                pattern: "*.log"
+            ],
+            [
+                path: { "${params.outdir}/umi_dedup/fastq_extracted_umi" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz",
+                enabled: params.save_umi_intermeds
+            ]
         ]
     }
-}
-
-//
-// Read QC and trimming options
-//
 
-process {
-    withName: 'MIRTRACE_RUN' {
+    //
+    // Make bowtie index
+    //
+    withName: 'INDEX_GENOME' {
         publishDir = [
-            path: { "${params.outdir}/mirtrace" },
+            path: { "${params.outdir}/bowtie_index/genome" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
 
-if (!(params.skip_fastqc)) {
-    process {
-        withName: '.*:FASTQC_UMITOOLS_FASTP:FASTQC_.*' {
-            ext.args = '--quiet'
-        }
+    //
+    // UMI deduplication
+    //
+    withName: '.*:DEDUPLICATE_UMIS:UMI_MAP_GENOME' {
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/bam_mapped" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: (
+                params.save_umi_intermeds
+            )
+        ]
     }
-}
-
-if (!params.skip_fastp) {
-    process {
-        withName: '.*:FASTQC_UMITOOLS_FASTP:FASTP' {
-                    ext.args = [ "",
-            params.trim_fastq              ? "" : "--disable_adapter_trimming",
-            params.clip_r1 > 0             ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.
-            params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.
-            params.fastp_min_length > 0    ? "-l ${params.fastp_min_length}" : "",
-            params.fastp_max_length > 0    ? "--max_len1 ${params.fastp_max_length}" : "",
-            params.three_prime_adapter == null ?  '' : "--adapter_sequence ${params.three_prime_adapter}"
-        ].join(" ").trim()
-            publishDir = [
-                [
-                    path: { "${params.outdir}/fastp" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.{json,html}"
-                ],
-                [
-                    path: { "${params.outdir}/fastp/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { "${params.outdir}/fastp" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fail.fastq.gz",
-                    enabled: params.save_trimmed_fail
-                ]
-            ]
-        }
-
+    withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/bam_mapped_sorted" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{bam}',
+            enabled: (
+                params.save_umi_intermeds
+            )
+        ]
     }
-
-    if (!params.skip_fastqc) {
-        process {
-            withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
-                ext.args = '--quiet'
-                publishDir = [
-                    path: { "${params.outdir}/fastqc/raw" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-            withName: '.*:.*:FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
-                ext.args = '--quiet'
-                publishDir = [
-                    path: { "${params.outdir}/fastqc/trim" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
+    withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/bam_mapped_sorted" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{bai,csi}',
+            enabled: (
+                params.save_umi_intermeds
+            )
+        ]
     }
-}
-
-if (params.with_umi && !params.skip_umi_extract) {
-    process {
-        withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:UMITOOLS_EXTRACT' {
-            ext.args   = [
-                    params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
-                    params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
-                ].join(' ').trim()
-            publishDir = [
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    enabled: params.save_umi_intermeds
-                ]
-            ]
-        }
+    withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:.*' {
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/bam_mapped_sorted" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{stats,flagstat,idxstats}'
+        ]
+    }
+    withName: '.*:DEDUPLICATE_UMIS:UMICOLLAPSE' {
+        ext.args = { meta.single_end ? "--algo ${params.umitools_method} --two-pass" : "--method ${params.umitools_method} --two-pass --paired --remove-unpaired --remove-chimeric" }
+        ext.prefix = { "${meta.id}.umi_dedup.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/bam_deduplicated" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: (
+                params.save_umi_intermeds
+            )
+        ]
+    }
+    withName: '.*:DEDUPLICATE_UMIS:SAMTOOLS_BAM2FQ' {
+        publishDir = [
+            path: { "${params.outdir}/umi_dedup/fastq_deduplicated" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: (
+                params.save_umi_intermeds
+            )
+        ]
     }
-}
-
-//
-// UMI tools deduplication
-//
-
-if (params.with_umi) {
-    process {
-        withName: '.*:DEDUPLICATE_UMIS:UMICOLLAPSE' {
-            ext.args = { meta.single_end ? "--algo ${params.umitools_method} --two-pass" : "--method ${params.umitools_method} --two-pass --paired --remove-unpaired --remove-chimeric" }
-            ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-            publishDir = [
-                path: { "${params.outdir}/umi_dedup" },
-                mode: params.publish_dir_mode,
-                pattern: '*.bam',
-                enabled: (
-                    params.save_umi_intermeds
-                )
-            ]
-        }
-
-        withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
-            ext.prefix = { "${meta.id}.sorted" }
-            publishDir = [
-                path: { "${params.outdir}/umi_dedup" },
-                mode: params.publish_dir_mode,
-                pattern: '*.{bam}',
-                enabled: (
-                    params.save_umi_intermeds
-                )
-            ]
-        }
-
-        withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-            ext.prefix = { "${meta.id}.sorted" }
-            publishDir = [
-                path: { "${params.outdir}/umi_dedup" },
-                mode: params.publish_dir_mode,
-                pattern: '*.{bai,csi}',
-                enabled: (
-                    params.save_umi_intermeds
-                )
-            ]
-        }
 
-        withName: '.*:DEDUPLICATE_UMIS:BAM_SORT_STATS_SAMTOOLS:.*' {
-            publishDir = [
-                path: { "${params.outdir}/umi_dedup/samtools_stats" },
-                mode: params.publish_dir_mode,
-                pattern: '*.{stats,flagstat,idxstats}'
-            ]
-        }
+    //
+    // MIRTRACE QC
+    //
+    withName: 'MIRTRACE_RUN' {
+        publishDir = [
+            //"mirtrace" already part of the published folder
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
-}
 
-//
-// Quantification
-//
+    //
+    // CONTAMINANT_FILTER
+    //
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:CONTAMINANT_FILTER:.*' {
+        publishDir = [
+            path: { "${params.outdir}/contaminant_filter/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 
-process {
+    //
+    // MIRNA_QUANT
+    //
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:FORMAT_.*' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/reference" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:PARSE_.*' {
-    publishDir = [
-            path: { "${params.outdir}/genome" },
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/reference" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:SAMTOOLS_SORT' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_MATURE' {
+        publishDir = [
+            path: { "${params.outdir}/bowtie_index/mirna_mature" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:INDEX_HAIRPIN' {
+        publishDir = [
+            path: { "${params.outdir}/bowtie_index/mirna_hairpin" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_MATURE' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/bam/mature" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_MATURE:.*' {
         ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
-            path: { "${params.outdir}/samtools" },
+            path: { "${params.outdir}/mirna_quant/bam/mature" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_.*:BAM_STATS_SAMTOOLS:.*' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_HAIRPIN' {
+        publishDir = [
+            path: { "${params.outdir}/mirna_quant/bam/hairpin" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BAM_STATS_HAIRPIN:.*' {
         ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
-            path: { "${params.outdir}/samtools/samtools_stats" },
+            path: { "${params.outdir}/mirna_quant/bam/hairpin" },
             mode: params.publish_dir_mode,
-            pattern: "*.{stats,flagstat,idxstats}"
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_.*' {
+    withName: 'EDGER_QC' {
         publishDir = [
-            path: { "${params.outdir}/unmapped/fastq" },
+            path: { "${params.outdir}/mirna_quant/edger_qc" },
             mode: params.publish_dir_mode,
-            pattern: "unmapped/*.gz"
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: 'SEQCLUSTER_SEQUENCES' {
         publishDir = [
-            path: { "${params.outdir}/seqcluster" },
-            enabled: false
+            path: { "${params.outdir}/mirna_quant/seqcluster" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'MIRTOP_QUANT' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:BOWTIE_MAP_SEQCLUSTER' {
         publishDir = [
-            path: { "${params.outdir}" },
+            path: { "${params.outdir}/mirna_quant/bam/seqcluster" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE' {
+    withName: 'MIRTOP_QUANT' {
         publishDir = [
-            path: { "${params.outdir}/mirtop" },
+            //mirtop already part of the output folder
+            path: { "${params.outdir}/mirna_quant/" },
             mode: params.publish_dir_mode,
-            pattern: "*.tsv"
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-    withName: 'EDGER_QC' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:TABLE_MERGE' {
         publishDir = [
-            path: { "${params.outdir}/edger" },
+            path: { "${params.outdir}/mirna_quant/mirtop" },
             mode: params.publish_dir_mode,
-            enabled: true
+            pattern: "*.tsv"
         ]
     }
-}
 
 
-process {
+    //
+    // GENOME_QUANT
+    //
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_.*' {
         ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
-            path: { "${params.outdir}/samtools" },
+            path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
     withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
         ext.prefix = { "${meta.id}.sorted" }
         publishDir = [
-            path: { "${params.outdir}/samtools/samtools_stats" },
+            path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,
             pattern: "*.{stats,flagstat,idxstats}"
         ]
     }
-    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_.*' {
+    withName: 'NFCORE_SMRNASEQ:SMRNASEQ:GENOME_QUANT:BOWTIE_MAP_GENOME' {
         publishDir = [
-            path: { "${params.outdir}/unmapped/fastq" },
+            path: { "${params.outdir}/genome_quant/bam" },
             mode: params.publish_dir_mode,
-            pattern: "unmapped/*.gz"
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-}
 
-if (!params.skip_mirdeep) {
-    process {
-        withName: 'MIRDEEP2_MAPPER' {
-            publishDir = [
-                path: { "${params.outdir}/mirdeep2/mapper" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-        withName: 'MIRDEEP2_RUN' {
-            publishDir = [
-                path: { "${params.outdir}/mirdeep2/run" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
 
-if (!params.skip_multiqc) {
-    process {
-        withName: 'MULTIQC' {
-            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 }
-            ]
-        }
+    //
+    // MIRDEEP
+    //
+    withName: 'MIRDEEP2_MAPPER' {
+        publishDir = [
+            path: { "${params.outdir}/mirdeep2/mapper" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+    withName: 'MIRDEEP2_RUN' {
+        publishDir = [
+            path: { "${params.outdir}/mirdeep2/run" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
+    //
+    // reports
+    //
+    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
+        publishDir = [
+            path: { "${params.outdir}/pipeline_info" },
+            mode: params.publish_dir_mode,
+            pattern: '*_versions.yml'
+        ]
+    }
+    withName: 'MULTIQC' {
+        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
 }