diff --git a/conf/modules.config b/conf/modules.config
index eaa35f259..d3c22f00c 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -41,8 +41,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -54,8 +53,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -64,8 +62,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -73,8 +70,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -83,8 +79,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -93,8 +88,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome/index" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -102,8 +96,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -111,8 +104,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -120,8 +112,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -129,8 +120,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/genome" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_reference
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
         ]
     }
 
@@ -138,8 +128,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/fastq" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: params.save_merged_fastq
+            saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
         ]
     }
 }
@@ -151,8 +140,7 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
             publishDir = [
                 path: { "${params.outdir}/genome/index" },
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-                enabled: params.save_reference
+                saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_reference ? filename : null }
             ]
         }
     }
@@ -167,9 +155,6 @@ process {
         ext.args   = '--record-count 1000000 --seed 1'
         ext.prefix = { "${meta.id}.subsampled" }
         publishDir = [
-            path: { "${params.outdir}/sample_fastq/fastq" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
     }
@@ -177,9 +162,6 @@ process {
     withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
         ext.args   = '--skipQuant'
         publishDir = [
-            path: { "${params.outdir}/sample_fastq/salmon" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename },
             enabled: false
         ]
     }
@@ -236,7 +218,7 @@ if (!params.skip_trimming) {
                         path: { "${params.outdir}/${params.trimmer}" },
                         mode: params.publish_dir_mode,
                         pattern: "*.fq.gz",
-                        enabled: params.save_trimmed
+                        saveAs: { params.save_trimmed ? it : null }
                     ],
                     [
                         path: { "${params.outdir}/${params.trimmer}" },
@@ -251,7 +233,7 @@ if (!params.skip_trimming) {
     if (params.trimmer == 'fastp') {
         process {
             withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
-                ext.args   = params.extra_fastp_args ?: ''
+                ext.args   = { params.extra_fastp_args ?: '' }
                 publishDir = [
                     [
                         path: { "${params.outdir}/${params.trimmer}" },
@@ -267,7 +249,7 @@ if (!params.skip_trimming) {
                         path: { "${params.outdir}/${params.trimmer}" },
                         mode: params.publish_dir_mode,
                         pattern: "*.fastq.gz",
-                        enabled: params.save_trimmed
+                        saveAs: { params.save_trimmed ? it : null }
                     ]
                 ]
             }
@@ -278,12 +260,12 @@ if (!params.skip_trimming) {
 if (params.with_umi && !params.skip_umi_extract) {
     process {
         withName: 'UMITOOLS_EXTRACT' {
-            ext.args   = [
+            ext.args   = { [
                     params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
                     params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
                     params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
                     params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-            ].join(' ').trim()
+            ].join(' ').trim() }
             publishDir = [
                 [
                     path: { "${params.outdir}/umitools" },
@@ -294,7 +276,7 @@ if (params.with_umi && !params.skip_umi_extract) {
                     path: { "${params.outdir}/umitools" },
                     mode: params.publish_dir_mode,
                     pattern: "*.fastq.gz",
-                    enabled: params.save_umi_intermeds
+                    saveAs: { params.save_umi_intermeds ? it : null }
                 ]
             ]
         }
@@ -319,7 +301,7 @@ if (!params.skip_bbsplit) {
                     path: { "${params.outdir}/bbsplit" },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
-                    enabled: params.save_bbsplit_reads
+                    saveAs: { params.save_bbsplit_reads ? it : null }
                 ]
             ]
         }
@@ -340,7 +322,7 @@ if (params.remove_ribo_rna) {
                     path: { "${params.outdir}/sortmerna" },
                     mode: params.publish_dir_mode,
                     pattern: "*.fastq.gz",
-                    enabled: params.save_non_ribo_reads
+                    saveAs: { params.save_non_ribo_reads ? it : null }
                 ]
             ]
         }
@@ -368,25 +350,21 @@ if (!params.skip_alignment) {
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.bam",
-                enabled: ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                    ( params.save_align_intermeds ||
-                        ( !params.with_umi && params.skip_markduplicates )
-                    )
-                ) || params.save_align_intermeds || params.skip_markduplicates
+                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
             ]
         }
 
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-            ext.args   = params.bam_csi_index ? '-c' : ''
+            ext.args   = { params.bam_csi_index ? '-c' : '' }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{bai,csi}",
-                enabled: ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                    ( params.save_align_intermeds ||
-                        ( !params.with_umi && params.skip_markduplicates )
-                    )
-                ) || params.save_align_intermeds || params.skip_markduplicates
+                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
+                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
+                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
             ]
         }
     }
@@ -411,7 +389,7 @@ if (!params.skip_alignment) {
             }
 
             withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
-                ext.args   = params.bam_csi_index ? '-c' : ''
+                ext.args   = { params.bam_csi_index ? '-c' : '' }
                 ext.prefix = { "${meta.id}.markdup.sorted" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
@@ -450,27 +428,19 @@ if (!params.skip_alignment) {
                         path: { "${params.outdir}/${params.aligner}" },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
-                        enabled: (
-                            params.save_align_intermeds ||
-                            params.with_umi ||
-                            params.save_umi_intermeds
-                        )
+                        saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
                     ]
                 ]
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
-                ext.args   = params.bam_csi_index ? '-c' : ''
+                ext.args   = { params.bam_csi_index ? '-c' : '' }
                 ext.prefix = { "${meta.id}.umi_dedup.sorted" }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.{bai,csi}',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.with_umi ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -490,7 +460,6 @@ if (!params.skip_alignment) {
             withName: 'BEDTOOLS_GENOMECOV' {
                 ext.args   = '-split -du'
                 publishDir = [
-                    path: { "${params.outdir}/bedtools/${meta.id}" },
                     enabled: false
                 ]
             }
@@ -498,7 +467,6 @@ if (!params.skip_alignment) {
             withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
                 ext.prefix = { "${meta.id}.clip.forward" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
                     enabled: false
                 ]
             }
@@ -515,7 +483,6 @@ if (!params.skip_alignment) {
             withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
                 ext.prefix = { "${meta.id}.clip.reverse" }
                 publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
                     enabled: false
                 ]
             }
@@ -534,10 +501,10 @@ if (!params.skip_alignment) {
     if (!params.skip_stringtie) {
         process {
             withName: 'STRINGTIE_STRINGTIE' {
-                ext.args   = [
+                ext.args   = { [
                     '-v',
                     params.stringtie_ignore_gtf ? '' : '-e'
-                ].join(' ').trim()
+                ].join(' ').trim() }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/stringtie" },
                     mode: params.publish_dir_mode,
@@ -555,7 +522,7 @@ if (!params.skip_alignment) {
 if (!params.skip_alignment && params.aligner == 'star_salmon') {
     process {
         withName: '.*:ALIGN_STAR:STAR_ALIGN|.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-            ext.args   = [
+            ext.args   = { [
                 '--quantMode TranscriptomeSAM',
                 '--twopassMode Basic',
                 '--outSAMtype BAM Unsorted',
@@ -568,7 +535,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 '--outSAMstrandField intronMotif',
                 params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
                 params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
-            ].flatten().unique(false).join(' ').trim()
+            ].flatten().unique(false).join(' ').trim() }
             publishDir = [
                 [
                     path: { "${params.outdir}/${params.aligner}/log" },
@@ -579,19 +546,19 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
-                    enabled: params.save_align_intermeds
+                    saveAs: { params.save_align_intermeds ? it : null }
                 ],
                 [
                     path: { "${params.outdir}/${params.aligner}/unmapped" },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
-                    enabled: params.save_unaligned
+                    saveAs: { params.save_unaligned ? it : null }
                 ]
             ]
         }
 
         withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
-            ext.args   = params.extra_salmon_quant_args ?: ''
+            ext.args   = { params.extra_salmon_quant_args ?: '' }
             publishDir = [
                 path: { "${params.outdir}/${params.aligner}" },
                 mode: params.publish_dir_mode,
@@ -633,10 +600,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -652,10 +616,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                         path: { "${params.outdir}/${params.aligner}" },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
-                        enabled: (
-                            params.save_align_intermeds ||
-                            params.save_umi_intermeds
-                        )
+                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                     ]
                 ]
             }
@@ -666,10 +627,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -678,10 +636,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bai',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -691,10 +646,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}/samtools_stats" },
                     mode: params.publish_dir_mode,
                     pattern: '*.{stats,flagstat,idxstats}',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -715,10 +667,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                         path: { "${params.outdir}/${params.aligner}" },
                         mode: params.publish_dir_mode,
                         pattern: '*.bam',
-                        enabled: (
-                            params.save_align_intermeds ||
-                            params.save_umi_intermeds
-                        )
+                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                     ]
                 ]
             }
@@ -728,10 +677,7 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bai',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
+                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
                 ]
             }
 
@@ -749,13 +695,13 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_STAR_SALMON' {
-                ext.args   = [
+                ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
                     "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim()
+                ].join(' ').trim() }
                 ext.args2  = 'star_salmon'
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
@@ -791,7 +737,7 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: "*.bam",
-                    enabled: params.save_align_intermeds
+                    saveAs: { params.save_align_intermeds ? it : null }
                 ],
                 [
                     path: { "${params.outdir}/${params.aligner}/log" },
@@ -813,13 +759,13 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_RSEM' {
-                ext.args   = [
+                ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
                     "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim()
+                ].join(' ').trim() }
                 ext.args2  = 'star_rsem'
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
@@ -849,13 +795,13 @@ if (!params.skip_alignment && params.aligner == 'hisat2') {
                     path: { "${params.outdir}/${params.aligner}" },
                     mode: params.publish_dir_mode,
                     pattern: '*.bam',
-                    enabled: params.save_align_intermeds
+                    saveAs: { params.save_align_intermeds ? it : null }
                 ],
                 [
                     path: { "${params.outdir}/${params.aligner}/unmapped" },
                     mode: params.publish_dir_mode,
                     pattern: '*.fastq.gz',
-                    enabled: params.save_unaligned
+                    saveAs: { params.save_unaligned ? it : null }
                 ]
             ]
         }
@@ -936,11 +882,11 @@ if (!params.skip_alignment && !params.skip_qc) {
     if (!params.skip_biotype_qc && params.featurecounts_group_type) {
         process {
             withName: 'SUBREAD_FEATURECOUNTS' {
-                ext.args   = [
+                ext.args   = { [
                     '-B -C',
                     params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
                     "-t $params.featurecounts_feature_type"
-                ].join(' ').trim()
+                ].join(' ').trim() }
                 publishDir = [
                     path: { "${params.outdir}/${params.aligner}/featurecounts" },
                     mode: params.publish_dir_mode,
@@ -1112,7 +1058,7 @@ if (!params.skip_alignment && !params.skip_qc) {
 if (!params.skip_multiqc) {
     process {
         withName: 'MULTIQC' {
-            ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+            ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
             publishDir = [
                 path: { [
                     "${params.outdir}/multiqc",
@@ -1132,7 +1078,7 @@ if (!params.skip_multiqc) {
 if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
     process {
         withName: '.*:QUANTIFY_SALMON:SALMON_QUANT' {
-            ext.args   = params.extra_salmon_quant_args ?: ''
+            ext.args   = { params.extra_salmon_quant_args ?: '' }
             publishDir = [
                 path: { "${params.outdir}/${params.pseudo_aligner}" },
                 mode: params.publish_dir_mode,
@@ -1168,13 +1114,13 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
     if (!params.skip_qc & !params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC_SALMON' {
-                ext.args   = [
+                ext.args   = { [
                     "--id_col 1",
                     "--sample_suffix ''",
                     "--outprefix deseq2",
                     "--count_col 3",
                     params.deseq2_vst ? '--vst TRUE' : ''
-                ].join(' ').trim()
+                ].join(' ').trim() }
                 ext.args2  = 'salmon'
                 publishDir = [
                     path: { "${params.outdir}/${params.pseudo_aligner}/deseq2_qc" },