diff --git a/conf/modules.config b/conf/modules.config
index 06a1e5a6..6b67b9aa 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,7 +21,8 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: 'NFCORE_CHIPSEQ:CHIPSEQ:INPUT_CHECK:SAMPLESHEET_CHECK' {
+    withName: 'SAMPLESHEET_CHECK' {
+        ext.args   = 'samplesheet.valid.csv'
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
             mode: params.publish_dir_mode,
@@ -36,6 +37,10 @@ process {
             pattern: '*_versions.yml'
         ]
     }
+
+    withName: 'KHMER_UNIQUEKMERS' {
+        publishDir = [ enabled: false ]
+    }
 }
 
 //
@@ -71,15 +76,6 @@ process {
         ]
     }
 
-    withName: 'UNTAR_CHROMAP_INDEX|CHROMAP_INDEX' {
-        publishDir = [
-            path: { "${params.outdir}/genome/index/chromap" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
-        ]
-    }
-
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
         publishDir = [
@@ -111,7 +107,8 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+            enabled: params.save_reference
         ]
     }
 }
@@ -258,6 +255,14 @@ if (params.aligner == 'bowtie2') {
 
 if (params.aligner == 'chromap') {
     process {
+        withName: 'CHROMAP_INDEX' {
+            publishDir = [
+                path: { "${params.outdir}/genome/index/${params.aligner}" },
+                mode: params.publish_dir_mode,
+                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+        }
+
         withName: CHROMAP_CHROMAP {
             ext.args   = '-l 2000 --low-mem --SAM'
             ext.prefix = { "${meta.id}.Lb" }
@@ -311,7 +316,12 @@ process {
     withName: 'PICARD_MERGESAMFILES' {
         ext.args   = '--SORT_ORDER coordinate --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
         ext.prefix = { "${meta.id}.mLb.sorted" }
-        publishDir = [ enabled: false ]
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/merged_library" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: params.save_align_intermeds
+        ]
     }
 
     withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
@@ -350,7 +360,6 @@ process {
         ]
     }
 
-    // Should only be published when paired end data is used and save_align_intermeds is true
     withName: 'BAMTOOLS_FILTER' {
         ext.args   = {
                 [
@@ -359,34 +368,41 @@ process {
                     params.keep_multi_map ? '' : '-q 1'
                 ].join(' ').trim()
         }
-        ext.prefix = { meta.single_end ?  "${meta.id}.mLb.noPublish" : "${meta.id}.mLb.flT.sorted" } //TODO check with atacseq
+        ext.prefix = { meta.single_end ? "${meta.id}.mLb.clN.sorted" : "${meta.id}.mLb.flT.sorted" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
+            path: { "${params.outdir}/${params.aligner}/merged_library" },
             mode: params.publish_dir_mode,
-            pattern: '*.mLb.flT.sorted.bam',
-            enabled: params.save_align_intermeds
+            pattern: '*.bam',
+            saveAs: { (meta.single_end || params.save_align_intermeds) ? "${it}" : null }
         ]
     }
 
     withName: 'BAM_REMOVE_ORPHANS' {
         ext.args   = '--only_fr_pairs'
         ext.prefix = { "${meta.id}.mLb.clN" }
-        publishDir = [ enabled: false ]
+        publishDir = [
+            path: { "${params.outdir}/${params.aligner}/merged_library" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: params.save_align_intermeds
+        ]
     }
 
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:SAMTOOLS_SORT' {
-        ext.prefix = { "${meta.id}.mLb.clN.sorted" }
+        ext.args   = '-n'
+        ext.prefix = { "${meta.id}.mLb.flT.name_sorted" }
         publishDir = [
             path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
             mode: params.publish_dir_mode,
-            pattern: '*.bam'
+            pattern: '*.bam',
+            enabled: params.save_align_intermeds
         ]
     }
 
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:SAMTOOLS_INDEX' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary" },
+            path: { "${params.outdir}/${params.aligner}/merged_library" },
             mode: params.publish_dir_mode,
             pattern: '*.{bai,csi}'
         ]
@@ -395,7 +411,7 @@ process {
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_FILTER_BAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
         ext.prefix = { "${meta.id}.mLb.clN.sorted.bam" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary/samtools_stats" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/samtools_stats" },
             mode: params.publish_dir_mode,
             pattern: "*.{stats,flagstat,idxstats}"
         ]
@@ -404,7 +420,7 @@ process {
     withName: 'PHANTOMPEAKQUALTOOLS' {
         ext.args2  = { "-p=$task.cpus" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary/phantompeakqualtools" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/phantompeakqualtools" },
             mode: params.publish_dir_mode,
             pattern: "*.{out,pdf}"
         ]
@@ -412,25 +428,33 @@ process {
 
     withName: 'MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS' {
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary/phantompeakqualtools" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/phantompeakqualtools" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: 'BEDTOOLS_GENOMECOV' {
-        ext.prefix = { "${meta.id}" }
+        ext.args   = { (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : '' }
+        ext.prefix = { "${meta.id}.mLB.clN" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig/scale" },
-            mode: params.publish_dir_mode,
-            pattern: "*.txt"
+            [
+                path: { "${params.outdir}/${params.aligner}/merged_library/bigwig" },
+                mode: params.publish_dir_mode,
+                pattern: "*.bigWig"
+            ],
+            [
+                path: { "${params.outdir}/${params.aligner}/merged_library/bigwig/scale" },
+                mode: params.publish_dir_mode,
+                pattern: "*.txt"
+            ]
         ]
     }
 
     withName: 'UCSC_BEDGRAPHTOBIGWIG' {
-        ext.prefix = { "${meta.id}" }
+        ext.prefix = { "${meta.id}.mLb.clN" }
         publishDir = [
-            path: { "${params.outdir}/${params.aligner}/mergedLibrary/bigwig" },
+            path: { "${params.outdir}/${params.aligner}/merged_library/bigwig" },
             mode: params.publish_dir_mode,
             pattern: "*.bigWig"
         ]
@@ -444,12 +468,12 @@ if (!params.skip_picard_metrics) {
             ext.prefix = { "${meta.id}.mLb.clN.sorted" }
             publishDir = [
                 [
-                    path: { "${params.outdir}/${params.aligner}/mergedLibrary/picard_metrics" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/picard_metrics" },
                     mode: params.publish_dir_mode,
                     pattern: "*_metrics"
                 ],
                 [
-                    path: { "${params.outdir}/${params.aligner}/mergedLibrary/picard_metrics/pdf" },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/picard_metrics/pdf" },
                     mode: params.publish_dir_mode,
                     pattern: "*.pdf"
                 ]
@@ -462,9 +486,9 @@ if (!params.skip_preseq) {
     process {
         withName: 'PRESEQ_LCEXTRAP' {
             ext.args   = '-verbose -bam -seed 1'
-            ext.prefix = { "${meta.id}.mLb.clN" }
+            ext.prefix = { "${meta.id}.mLb.mkD" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/preseq" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/preseq" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -475,10 +499,10 @@ if (!params.skip_preseq) {
 if (!params.skip_plot_profile) {
     process {
         withName: 'DEEPTOOLS_COMPUTEMATRIX' {
-            ext.args   = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --skipZeros --smartLabels'
+            ext.args   = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/deepTools/plotProfile" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -487,7 +511,7 @@ if (!params.skip_plot_profile) {
         withName: 'DEEPTOOLS_PLOTPROFILE' {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/deepTools/plotProfile" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -496,7 +520,7 @@ if (!params.skip_plot_profile) {
         withName: 'DEEPTOOLS_PLOTHEATMAP' {
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/deepTools/plotProfile" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotProfile" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -504,12 +528,6 @@ if (!params.skip_plot_profile) {
     }
 }
 
-process {
-    withName: 'KHMER_UNIQUEKMERS' {
-        publishDir = [ enabled: false ]
-    }
-}
-
 if (!params.skip_plot_fingerprint) {
     process {
         withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
@@ -520,7 +538,7 @@ if (!params.skip_plot_fingerprint) {
             ].join(' ').trim() }
             ext.prefix = { "${meta.id}.mLb.clN" }
             publishDir = [
-                path: { "${params.outdir}/${params.aligner}/mergedLibrary/deepTools/plotFingerprint" },
+                path: { "${params.outdir}/${params.aligner}/merged_library/deepTools/plotFingerprint" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -536,11 +554,11 @@ process {
             params.save_macs_pileup     ? '--bdg --SPMR' : '',
             params.macs_fdr             ? "--qvalue ${params.macs_fdr}" : '',
             params.macs_pvalue          ? "--pvalue ${params.macs_pvalue}" : '',
-            params.aligner == "chromap" ? "--format BAM" : ''
+            params.aligner == "chromap" ? "--format BAM" : '' //TODO check if not needed anymore with new chromap versions
         ].join(' ').trim()
         publishDir = [
             path: { [
-                "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
+                "${params.outdir}/${params.aligner}/merged_library/macs2",
                 params.narrow_peak? '/narrowPeak' : '/broadPeak'
             ].join('') },
             mode: params.publish_dir_mode,
@@ -551,22 +569,14 @@ process {
     withName: 'FRIP_SCORE' {
         ext.args   = '-bed -c -f 0.20'
         publishDir = [
-            path: { [
-                "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                '/qc'
-            ].join('') },
+            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/qc" },
             enabled: false
         ]
     }
 
     withName: 'MULTIQC_CUSTOM_PEAKS' {
         publishDir = [
-            path: { [
-                "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                '/qc'
-            ].join('') },
+            path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak} ? '/narrowPeak' : '/broadPeak'}/qc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -579,10 +589,7 @@ if (!params.skip_peak_annotation) {
             ext.args   = '-gid'
             ext.prefix = { "${meta.id}_peaks" }
             publishDir = [
-                path: { [
-                    "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak? '/narrowPeak' : '/broadPeak'
-                ].join('') },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak' }" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -594,11 +601,7 @@ if (!params.skip_peak_annotation) {
             withName: 'PLOT_MACS2_QC' {
                 ext.args   = '-o ./ -p macs2_peak'
                 publishDir = [
-                    path: { [
-                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/qc'
-                    ].join('') },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrow_peak' : '/broad_peak'}/qc" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -608,11 +611,7 @@ if (!params.skip_peak_annotation) {
                 ext.args   = '-o ./'
                 ext.prefix = 'macs2_annotatePeaks'
                 publishDir = [
-                    path: { [
-                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/qc'
-                    ].join('') },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/qc" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -627,12 +626,7 @@ if (!params.skip_consensus_peaks) {
             ext.when   = { meta.multiple_groups || meta.replicates_exist }
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
-                path: { [
-                    "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                    '/consensus',
-                    "/${meta.id}"
-                ].join('') },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/consensus/${meta.id}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -642,12 +636,7 @@ if (!params.skip_consensus_peaks) {
             ext.args   = '-F SAF -O --fracOverlap 0.2'
             ext.prefix = { "${meta.id}.consensus_peaks" }
             publishDir = [
-                path: { [
-                    "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                    params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                    '/consensus',
-                    "/${meta.id}"
-                ].join('') },
+                path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak? '/narrowPeak' : '/broadPeak'}/consensus/${meta.id}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
@@ -660,12 +649,7 @@ if (!params.skip_consensus_peaks) {
                 ext.args   = '-gid'
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { [
-                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/consensus',
-                        "/${meta.id}"
-                    ].join('') },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/consensus/${meta.id}" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -674,12 +658,7 @@ if (!params.skip_consensus_peaks) {
             withName: 'ANNOTATE_BOOLEAN_PEAKS' {
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { [
-                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/consensus',
-                        "/${meta.id}"
-                    ].join('') },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/consensus/${meta.id}" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -699,13 +678,7 @@ if (!params.skip_consensus_peaks) {
                 ].join(' ').trim()
                 ext.prefix = { "${meta.id}.consensus_peaks" }
                 publishDir = [
-                    path: { [
-                        "${params.outdir}/${params.aligner}/mergedLibrary/macs2",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak',
-                        '/consensus',
-                        "/${meta.id}",
-                        '/deseq2'
-                    ].join('') },
+                    path: { "${params.outdir}/${params.aligner}/merged_library/macs2/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}/consensus/${meta.id}/deseq2" },
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ]
@@ -718,12 +691,16 @@ if (!params.skip_igv) {
     process {
         withName: 'IGV' {
             publishDir = [
-                    path: { [
-                        "${params.outdir}/igv",
-                        params.narrow_peak? '/narrowPeak' : '/broadPeak'
-                    ].join('') },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                [
+                        path: { "${params.outdir}/igv/${params.narrow_peak? '/narrowPeak' : '/broadPeak' }" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.{txt,xml}'
+                ],
+                [
+                        path: { "${params.outdir}/genome" },
+                        mode: params.publish_dir_mode,
+                        pattern: '*.{fa,fasta}'
+                ]
             ]
         }
     }
@@ -734,10 +711,7 @@ if (!params.skip_multiqc) {
         withName: 'MULTIQC' {
             ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
             publishDir = [
-                path: { [
-                    "${params.outdir}/multiqc",
-                    params.narrow_peak? '/narrowPeak' : '/broadPeak'
-                ].join('') },
+                path: { "${params.outdir}/multiqc/${params.narrow_peak ? '/narrowPeak' : '/broadPeak'}" },
                 mode: params.publish_dir_mode,
                 saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
diff --git a/docs/output.md b/docs/output.md
index b3198554..065dcfd3 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -108,19 +108,19 @@ The library-level alignments associated with the same sample are merged and subs
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/`
+- `<ALIGNER>/merged_library/`
   - `*.bam`: Merged library-level, coordinate sorted `*.bam` files after the marking of duplicates, and filtering based on various criteria. The file suffix for the final filtered files will be `*.mLb.clN.*`. If you specify the `--save_align_intermeds` parameter then two additional sets of files will be present. These represent the unfiltered alignments with duplicates marked (`*.mLb.mkD.*`), and in the case of paired-end datasets the filtered alignments before the removal of orphan read pairs (`*.mLb.flT.*`).
-- `<ALIGNER>/mergedLibrary/samtools_stats/`
+- `<ALIGNER>/merged_library/samtools_stats/`
   - SAMtools `*.flagstat`, `*.idxstats` and `*.stats` files generated from the alignment files.
-- `<ALIGNER>/mergedLibrary/picard_metrics/`
+- `<ALIGNER>/merged_library/picard_metrics/`
   - `*_metrics`: Alignment QC files from picard CollectMultipleMetrics.
   - `*.metrics.txt`: Metrics file from MarkDuplicates.
-- `<ALIGNER>/mergedLibrary/picard_metrics/pdf/`
+- `<ALIGNER>/merged_library/picard_metrics/pdf/`
   - `*.pdf`: Alignment QC plot files from picard CollectMultipleMetrics.
-- `<ALIGNER>/mergedLibrary/preseq/`
+- `<ALIGNER>/merged_library/preseq/`
   - `*.lc_extrap.txt`: Preseq expected future yield file.
 
-> **NB:** File names in the resulting directory (i.e. `<ALIGNER>/mergedLibrary/`) will have the '`.mLb.`' suffix.
+> **NB:** File names in the resulting directory (i.e. `<ALIGNER>/merged_library/`) will have the '`.mLb.`' suffix.
 
 </details>
 
@@ -141,7 +141,7 @@ The [Preseq](http://smithlabresearch.org/software/preseq/) package is aimed at p
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/bigwig/`
+- `<ALIGNER>/merged_library/bigwig/`
   - `*.bigWig`: Normalised bigWig files scaled to 1 million mapped reads.
 
 </details>
@@ -153,12 +153,12 @@ The [bigWig](https://genome.ucsc.edu/goldenpath/help/bigWig.html) format is in a
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/phantompeakqualtools/`
+- `<ALIGNER>/merged_library/phantompeakqualtools/`
   - `*.spp.out`, `*.spp.pdf`: phantompeakqualtools output files.
   - `*_mqc.tsv`: MultiQC custom content files.
-- `<ALIGNER>/mergedLibrary/deepTools/plotFingerprint/`
+- `<ALIGNER>/merged_library/deepTools/plotFingerprint/`
   - `*.plotFingerprint.pdf`, `*.plotFingerprint.qcmetrics.txt`, `*.plotFingerprint.raw.txt`: plotFingerprint output files.
-- `<ALIGNER>/mergedLibrary/deepTools/plotProfile/`
+- `<ALIGNER>/merged_library/deepTools/plotProfile/`
   - `*.computeMatrix.mat.gz`, `*.computeMatrix.vals.mat.tab`, `*.plotProfile.pdf`, `*.plotProfile.tab`, `*.plotHeatmap.pdf`, `*.plotHeatmap.mat.tab`: plotProfile output files.
 
 </details>
@@ -188,10 +188,10 @@ The results from deepTools plotProfile gives you a quick visualisation for the g
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/`
+- `<ALIGNER>/merged_library/macs2/<PEAK_TYPE>/`
   - `*.xls`, `*.broadPeak` or `*.narrowPeak`, `*.gappedPeak`, `*summits.bed`: MACS2 output files - the files generated will depend on whether MACS2 has been run in _narrowPeak_ or _broadPeak_ mode.
   - `*.annotatePeaks.txt`: HOMER peak-to-gene annotation file.
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/qc/`
+- `<ALIGNER>/merged_library/macs2/<PEAK_TYPE>/qc/`
   - `macs2_peak.plots.pdf`: QC plots for MACS2 peaks.
   - `macs2_annotatePeaks.plots.pdf`: QC plots for peak-to-gene feature annotation.
   - `*.FRiP_mqc.tsv`, `*.peak_count_mqc.tsv`, `annotatepeaks.summary_mqc.tsv`: MultiQC custom-content files for FRiP score, peak count and peak-to-gene ratios.
@@ -217,7 +217,7 @@ Various QC plots per sample including number of peaks, fold-change distribution,
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/`
+- `<ALIGNER>/merged_library/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/`
   - `*.bed`: Consensus peak-set across all samples in BED format.
   - `*.saf`: Consensus peak-set across all samples in SAF format. Required by featureCounts for read quantification.
   - `*.featureCounts.txt`: Read counts across all samples relative to consensus peak-set.
@@ -245,7 +245,7 @@ The [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) tool is used to co
 <details markdown="1">
     <summary>Output files</summary>
 
-- `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/deseq2/`
+- `<ALIGNER>/merged_library/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/deseq2/`
   - `*.sample.dists.txt`: Spreadsheet containing sample-to-sample distance across each consensus peak.
   - `*.plots.pdf`: File containing PCA and hierarchical clustering plots.
   - `*.dds.RData`: File containing R `DESeqDataSet` object generated by DESeq2, with either
@@ -254,7 +254,7 @@ The [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) tool is used to co
     `readRDS` to give user control of the eventual object name.
   - `*pca.vals.txt`: Matrix of values for the first 2 principal components.
   - `R_sessionInfo.log`: File containing information about R, the OS and attached or loaded packages.
-  - `<ALIGNER>/mergedLibrary/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/sizeFactors/`
+  - `<ALIGNER>/merged_library/macs2/<PEAK_TYPE>/consensus/<ANTIBODY>/sizeFactors/`
   - `*.txt`, `*.RData`: Files containing DESeq2 sizeFactors per sample.
 
 </details>
diff --git a/modules/local/bam_remove_orphans.nf b/modules/local/bam_remove_orphans.nf
index 95a56c60..d6e221aa 100644
--- a/modules/local/bam_remove_orphans.nf
+++ b/modules/local/bam_remove_orphans.nf
@@ -17,6 +17,9 @@ process BAM_REMOVE_ORPHANS {
     tuple val(meta), path("${prefix}.bam"), emit: bam
     path "versions.yml"                   , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     def args = task.ext.args ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/local/bedtools_genomecov.nf b/modules/local/bedtools_genomecov.nf
index 2f38c06c..28dcc5dd 100644
--- a/modules/local/bedtools_genomecov.nf
+++ b/modules/local/bedtools_genomecov.nf
@@ -15,11 +15,13 @@ process BEDTOOLS_GENOMECOV {
     tuple val(meta), path("*.txt")     , emit: scale_factor
     path "versions.yml"                , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
+    def args   = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     def pe     = meta.single_end ? '' : '-pc'
-    def extend = (meta.single_end && params.fragment_size > 0) ? "-fs ${params.fragment_size}" : ''
     """
     SCALE_FACTOR=\$(grep '[0-9] mapped (' $flagstat | awk '{print 1000000/\$1}')
     echo \$SCALE_FACTOR > ${prefix}.scale_factor.txt
@@ -30,7 +32,7 @@ process BEDTOOLS_GENOMECOV {
         -bg \\
         -scale \$SCALE_FACTOR \\
         $pe \\
-        $extend \\
+        $args \\
         | sort -T '.' -k1,1 -k2,2n > ${prefix}.bedGraph
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/modules/local/deseq2_qc.nf b/modules/local/deseq2_qc.nf
index fe389300..d9b96e11 100644
--- a/modules/local/deseq2_qc.nf
+++ b/modules/local/deseq2_qc.nf
@@ -26,10 +26,12 @@ process DESEQ2_QC {
     path "size_factors"         , optional:true, emit: size_factors
     path "versions.yml"         , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
-    def args      = task.ext.args ?: ''
-    def peak_type = params.narrow_peak ? 'narrowPeak' : 'broadPeak'
-    def prefix    = task.ext.prefix ?: "${meta.id}"
+    def args   = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     deseq2_qc.r \\
         --count_file $counts \\
diff --git a/modules/local/frip_score.nf b/modules/local/frip_score.nf
index ffcc6e2d..28133e0c 100644
--- a/modules/local/frip_score.nf
+++ b/modules/local/frip_score.nf
@@ -14,6 +14,9 @@ process FRIP_SCORE {
     tuple val(meta), path("*.txt"), emit: txt
     path "versions.yml"           , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = task.ext.args   ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
diff --git a/modules/local/genome_blacklist_regions.nf b/modules/local/genome_blacklist_regions.nf
index 4421fb6c..fcb8451c 100644
--- a/modules/local/genome_blacklist_regions.nf
+++ b/modules/local/genome_blacklist_regions.nf
@@ -17,6 +17,9 @@ process GENOME_BLACKLIST_REGIONS {
     path '*.bed'       , emit: bed
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def file_out = "${sizes.simpleName}.include_regions.bed"
     if (blacklist) {
diff --git a/modules/local/gtf2bed.nf b/modules/local/gtf2bed.nf
index 91e29062..8a8e7bf9 100644
--- a/modules/local/gtf2bed.nf
+++ b/modules/local/gtf2bed.nf
@@ -14,6 +14,9 @@ process GTF2BED {
     path '*.bed'       , emit: bed
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     """
     gtf2bed \\
diff --git a/modules/local/igv.nf b/modules/local/igv.nf
index 59a2d2e8..cf02fd9e 100644
--- a/modules/local/igv.nf
+++ b/modules/local/igv.nf
@@ -20,8 +20,12 @@ process IGV {
     output:
     path "*files.txt"  , emit: txt
     path "*.xml"       , emit: xml
+    path fasta         , emit: fasta
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // scripts are bundled with the pipeline in nf-core/chipseq/bin/
     def consensus_dir = "${aligner_dir}/mergedLibrary/macs2/${peak_dir}/consensus/*"
     """
diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf
index 31552551..d23d2cbe 100644
--- a/modules/local/multiqc.nf
+++ b/modules/local/multiqc.nf
@@ -56,6 +56,9 @@ process MULTIQC {
     path "*_plots"             , optional:true, emit: plots
     path "versions.yml"        , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args          = task.ext.args ?: ''
     def custom_config = params.multiqc_config ? "--config $mqc_custom_config" : ''
diff --git a/modules/local/multiqc_custom_peaks.nf b/modules/local/multiqc_custom_peaks.nf
index 8fabe949..c19d81a5 100644
--- a/modules/local/multiqc_custom_peaks.nf
+++ b/modules/local/multiqc_custom_peaks.nf
@@ -14,6 +14,9 @@ process MULTIQC_CUSTOM_PEAKS {
     tuple val(meta), path("*.peak_count_mqc.tsv"), emit: count
     tuple val(meta), path("*.FRiP_mqc.tsv")      , emit: frip
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
diff --git a/modules/local/multiqc_custom_phantompeakqualtools.nf b/modules/local/multiqc_custom_phantompeakqualtools.nf
index c7f4127f..9e59d057 100644
--- a/modules/local/multiqc_custom_phantompeakqualtools.nf
+++ b/modules/local/multiqc_custom_phantompeakqualtools.nf
@@ -16,6 +16,9 @@ process MULTIQC_CUSTOM_PHANTOMPEAKQUALTOOLS {
     tuple val(meta), path("*.spp_rsc_mqc.tsv")        , emit: rsc
     tuple val(meta), path("*.spp_correlation_mqc.tsv"), emit: correlation
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
diff --git a/modules/local/plot_homer_annotatepeaks.nf b/modules/local/plot_homer_annotatepeaks.nf
index eed17949..36c4730e 100644
--- a/modules/local/plot_homer_annotatepeaks.nf
+++ b/modules/local/plot_homer_annotatepeaks.nf
@@ -17,6 +17,9 @@ process PLOT_HOMER_ANNOTATEPEAKS {
     path '*.tsv'       , emit: tsv
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "annotatepeaks"
diff --git a/modules/local/plot_macs2_qc.nf b/modules/local/plot_macs2_qc.nf
index 92f400d5..7599c9f8 100644
--- a/modules/local/plot_macs2_qc.nf
+++ b/modules/local/plot_macs2_qc.nf
@@ -8,15 +8,19 @@ process PLOT_MACS2_QC {
 
     input:
     path peaks
+    val is_narrow_peak
 
     output:
     path '*.txt'       , emit: txt
     path '*.pdf'       , emit: pdf
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
     def args      = task.ext.args ?: ''
-    def peak_type = params.narrow_peak ? 'narrowPeak' : 'broadPeak'
+    def peak_type = is_narrow_peak ? 'narrowPeak' : 'broadPeak'
     """
     plot_macs2_qc.r \\
         -i ${peaks.join(',')} \\
diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
index c28658f5..216e9fb7 100644
--- a/modules/local/samplesheet_check.nf
+++ b/modules/local/samplesheet_check.nf
@@ -18,10 +18,11 @@ process SAMPLESHEET_CHECK {
     task.ext.when == null || task.ext.when
 
     script: // This script is bundled with the pipeline, in nf-core/chipseq/bin/
+    def args = task.ext.args ?: ''
     """
     check_samplesheet.py \\
         $samplesheet \\
-        samplesheet.valid.csv
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/star_genomegenerate.nf b/modules/local/star_genomegenerate.nf
index 904b0714..285df97c 100644
--- a/modules/local/star_genomegenerate.nf
+++ b/modules/local/star_genomegenerate.nf
@@ -16,6 +16,9 @@ process STAR_GENOMEGENERATE {
     path "star"        , emit: index
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     def args   = (task.ext.args ?: '').tokenize()
     def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
diff --git a/subworkflows/local/prepare_genome.nf b/subworkflows/local/prepare_genome.nf
index dd16e1f5..bd7033cb 100644
--- a/subworkflows/local/prepare_genome.nf
+++ b/subworkflows/local/prepare_genome.nf
@@ -41,13 +41,7 @@ workflow PREPARE_GENOME {
         ch_fasta    = GUNZIP_FASTA ( [ [:], params.fasta ] ).gunzip.map{ it[1] }
         ch_versions = ch_versions.mix(GUNZIP_FASTA.out.versions)
     } else {
-        ch_fasta = file(params.fasta)
-    }
-
-    // Make fasta file available if reference saved or IGV is run
-    if (params.save_reference || !params.skip_igv) {
-        file("${params.outdir}/genome/").mkdirs()
-        ch_fasta.copyTo("${params.outdir}/genome/")
+        ch_fasta = Channel.value(file(params.fasta))
     }
 
     //
@@ -107,14 +101,15 @@ workflow PREPARE_GENOME {
             ch_gene_bed = GUNZIP_GENE_BED ( [ [:], params.gene_bed ] ).gunzip.map{ it[1] }
             ch_versions = ch_versions.mix(GUNZIP_GENE_BED.out.versions)
         } else {
-            ch_gene_bed = file(params.gene_bed)
+            ch_gene_bed = Channel.value(file(params.gene_bed))
         }
     }
 
     //
     // Create chromosome sizes file
     //
-    ch_chrom_sizes = CUSTOM_GETCHROMSIZES ( [ [:], ch_fasta ] ).sizes.map{ it[1] }
+    CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
+    ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
     ch_fai         = CUSTOM_GETCHROMSIZES.out.fai.map{ it[1] }
     ch_versions    = ch_versions.mix(CUSTOM_GETCHROMSIZES.out.versions)
 
@@ -144,7 +139,7 @@ workflow PREPARE_GENOME {
                 ch_bwa_index = file(params.bwa_index)
             }
         } else {
-            ch_bwa_index = BWA_INDEX ( [ [:], ch_fasta ] ).index
+            ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
             ch_versions  = ch_versions.mix(BWA_INDEX.out.versions)
         }
     }
@@ -162,7 +157,7 @@ workflow PREPARE_GENOME {
                 ch_bowtie2_index = [ [:], file(params.bowtie2_index) ]
             }
         } else {
-            ch_bowtie2_index = BOWTIE2_BUILD ( [ [:], ch_fasta ] ).index
+            ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index
             ch_versions      = ch_versions.mix(BOWTIE2_BUILD.out.versions)
         }
     }
@@ -180,7 +175,7 @@ workflow PREPARE_GENOME {
                 ch_chromap_index = [ [:], file(params.chromap_index) ]
             }
         } else {
-            ch_chromap_index = CHROMAP_INDEX ( [ [:], ch_fasta ] ).index
+            ch_chromap_index = CHROMAP_INDEX ( ch_fasta.map { [ [:], it ] } ).index
             ch_versions  = ch_versions.mix(CHROMAP_INDEX.out.versions)
         }
     }
@@ -195,7 +190,7 @@ workflow PREPARE_GENOME {
                 ch_star_index = UNTAR_STAR_INDEX ( [ [:], params.star_index ] ).untar.map{ it[1] }
                 ch_versions   = ch_versions.mix(UNTAR_STAR_INDEX.out.versions)
             } else {
-                ch_star_index = file(params.star_index)
+                ch_star_index = Channel.value(file(params.star_index))
             }
         } else {
             ch_star_index = STAR_GENOMEGENERATE ( ch_fasta, ch_gtf ).index
diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
index fc914a51..01ff8545 100644
--- a/workflows/chipseq.nf
+++ b/workflows/chipseq.nf
@@ -205,7 +205,7 @@ workflow CHIPSEQ {
         ch_samtools_stats    = FASTQ_ALIGN_BOWTIE2.out.stats
         ch_samtools_flagstat = FASTQ_ALIGN_BOWTIE2.out.flagstat
         ch_samtools_idxstats = FASTQ_ALIGN_BOWTIE2.out.idxstats
-        ch_versions = ch_versions.mix(FASTQ_ALIGN_BOWTIE2.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQ_ALIGN_BOWTIE2.out.versions)
     }
 
     //
@@ -229,7 +229,7 @@ workflow CHIPSEQ {
         ch_samtools_stats    = FASTQ_ALIGN_CHROMAP.out.stats
         ch_samtools_flagstat = FASTQ_ALIGN_CHROMAP.out.flagstat
         ch_samtools_idxstats = FASTQ_ALIGN_CHROMAP.out.idxstats
-        ch_versions = ch_versions.mix(FASTQ_ALIGN_CHROMAP.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQ_ALIGN_CHROMAP.out.versions)
     }
 
     //
@@ -274,7 +274,7 @@ workflow CHIPSEQ {
     PICARD_MERGESAMFILES (
         ch_sort_bam
     )
-    ch_versions = ch_versions.mix(PICARD_MERGESAMFILES.out.versions.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(PICARD_MERGESAMFILES.out.versions.first())
 
     //
     // SUBWORKFLOW: Mark duplicates & filter BAM files after merging
@@ -549,7 +549,8 @@ workflow CHIPSEQ {
             // MODULE: MACS2 QC plots with R
             //
             PLOT_MACS2_QC (
-                ch_macs2_peaks.collect{it[1]}
+                ch_macs2_peaks.collect{it[1]},
+                params.narrow_peak
             )
             ch_versions = ch_versions.mix(PLOT_MACS2_QC.out.versions)