diff --git a/conf/modules.config b/conf/modules.config
index 4f86f82ac..9d1152ac1 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -23,323 +23,3 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 }
-
-//
-// General alignment options
-//
-
-if (!params.skip_alignment) {
-    process {
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
-            ext.prefix = { "${meta.id}.sorted.bam" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                mode: params.publish_dir_mode,
-                pattern: "*.{stats,flagstat,idxstats}"
-            ]
-        }
-
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
-            ext.prefix = { "${meta.id}.sorted" }
-            publishDir = [
-                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
-            ]
-        }
-
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-            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
-            ]
-        }
-    }
-
-    if (!params.skip_markduplicates && !params.with_umi) {
-        process {
-            withName: '.*:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.markdup.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-
-    if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
-        process {
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
-                ext.args   = { [
-                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
-                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-                ].join(' ').trim() }
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        enabled: (
-                            params.save_align_intermeds ||
-                            params.with_umi ||
-                            params.save_umi_intermeds
-                        )
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:SAMTOOLS_INDEX' {
-                ext.args   = params.bam_csi_index ? '-c' : ''
-                ext.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.with_umi ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-
-    if (!params.skip_bigwig) {
-        process {
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
-                ext.prefix = { "${meta.id}.clip.forward" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
-                ext.prefix = { "${meta.id}.forward" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
-                ext.prefix = { "${meta.id}.clip.reverse" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    enabled: false
-                ]
-            }
-
-            withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
-                ext.prefix = { "${meta.id}.reverse" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/bigwig" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
-
-//
-// STAR Salmon alignment options
-//
-
-if (!params.skip_alignment && params.aligner == 'star_salmon') {
-    process {
-        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
-            ext.args   = params.extra_salmon_quant_args ?: ''
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_STAR_SALMON:SALMON_SE_.*' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (params.with_umi) {
-        process {
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
-                ext.prefix = { "${meta.id}.transcriptome.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
-                publishDir = [
-                    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
-                    )
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
-                ext.args   = { [
-                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-                    params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
-                    params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
-                ].join(' ').trim() }
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        enabled: (
-                            params.save_align_intermeds ||
-                            params.save_umi_intermeds
-                        )
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    enabled: (
-                        params.save_align_intermeds ||
-                        params.save_umi_intermeds
-                    )
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
-                ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
-    }
-}
-
-//
-// Salmon pseudo-alignment options
-//
-
-if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
-    process {
-        withName: '.*:QUANTIFY_SALMON:SALMON_QUANT' {
-            ext.args   = params.extra_salmon_quant_args ?: ''
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_SALMON:SALMON_TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_SALMON:SALMON_TXIMPORT' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
-        withName: '.*:QUANTIFY_SALMON:SALMON_SE_.*' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-}
diff --git a/subworkflows/local/align_star.nf b/subworkflows/local/align_star.nf
index 25e44dfd7..f9fab4b4d 100644
--- a/subworkflows/local/align_star.nf
+++ b/subworkflows/local/align_star.nf
@@ -48,18 +48,18 @@ workflow ALIGN_STAR {
     ].flatten().unique(false).join(' ').trim()
     align_publish_dir = [
         [
-            path: { "${params.outdir}/${params.aligner}/log" },
+            path: "${params.outdir}/${params.aligner}/log",
             mode: params.publish_dir_mode,
             pattern: '*.{out,tab}'
         ],
         [
-            path: { "${params.outdir}/${params.aligner}" },
+            path: "${params.outdir}/${params.aligner}",
             mode: params.publish_dir_mode,
             pattern: '*.bam',
             enabled: params.save_align_intermeds
         ],
         [
-            path: { "${params.outdir}/${params.aligner}/unmapped" },
+            path: "${params.outdir}/${params.aligner}/unmapped",
             mode: params.publish_dir_mode,
             pattern: '*.fastq.gz',
             enabled: params.save_unaligned
@@ -96,7 +96,40 @@ workflow ALIGN_STAR {
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
     //
-    BAM_SORT_STATS_SAMTOOLS ( ch_orig_bam, fasta )
+    sort_ext_prefix  = { "${meta.id}.sorted" }
+    sort_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.bam",
+        enabled: ( !params.with_umi && params.skip_markduplicates ) ||
+            params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    index_ext_args = params.bam_csi_index ? '-c' : ''
+    index_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.{bai,csi}",
+        enabled: ( !params.with_umi && params.skip_markduplicates ) ||
+            params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    stats_ext_prefix = { "${meta.id}.sorted.bam" }
+    stats_publish_dir = [
+        path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
+        pattern: "*.{stats,flagstat,idxstats}"
+    ]
+    BAM_SORT_STATS_SAMTOOLS (
+        ch_orig_bam,
+        fasta,
+        sort_ext_prefix,
+        sort_publish_dir,
+        index_ext_args,
+        index_publish_dir,
+        stats_ext_prefix,
+        stats_publish_dir
+    )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
     emit:
diff --git a/subworkflows/local/quantify_rsem.nf b/subworkflows/local/quantify_rsem.nf
index 0dc0934b7..53a2fe8c6 100644
--- a/subworkflows/local/quantify_rsem.nf
+++ b/subworkflows/local/quantify_rsem.nf
@@ -50,7 +50,38 @@ workflow QUANTIFY_RSEM {
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
     //
-    BAM_SORT_STATS_SAMTOOLS ( RSEM_CALCULATEEXPRESSION.out.bam_star, fasta )
+    sort_ext_prefix = { "${meta.id}.sorted" }
+    sort_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.bam",
+        enabled: params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    index_ext_args = params.bam_csi_index ? '-c' : ''
+    index_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.{bai,csi}",
+        enabled: params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    stats_ext_prefix = { "${meta.id}.sorted.bam" }
+    stats_publish_dir = [
+        path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
+        pattern: "*.{stats,flagstat,idxstats}"
+    ]
+    BAM_SORT_STATS_SAMTOOLS (
+        RSEM_CALCULATEEXPRESSION.out.bam_star,
+        fasta,
+        sort_ext_prefix,
+        sort_publish_dir,
+        index_ext_args,
+        index_publish_dir,
+        stats_ext_prefix,
+        stats_publish_dir
+    )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
     //
diff --git a/subworkflows/local/quantify_salmon.nf b/subworkflows/local/quantify_salmon.nf
index 4ab996b2c..f156b2b1b 100644
--- a/subworkflows/local/quantify_salmon.nf
+++ b/subworkflows/local/quantify_salmon.nf
@@ -19,23 +19,39 @@ workflow QUANTIFY_SALMON {
     gtf              // channel: /path/to/genome.gtf
     alignment_mode   //    bool: Run Salmon in alignment mode
     lib_type         //     val: String to override salmon library type
+    publish_dir_path
 
     main:
 
     ch_versions = Channel.empty()
 
+    publish_dir = [
+        path: publish_dir_path,
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
+
     //
     // Quantify and merge counts across samples
     //
+    SALMON_QUANT.config.ext.args = params.extra_salmon_quant_args ?: ''
+    SALMON_QUANT.config.publishDir = [
+        path: publish_dir_path,
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('_meta_info.json') ? null : filename }
+    ]
     SALMON_QUANT ( reads, index, gtf, transcript_fasta, alignment_mode, lib_type )
     ch_versions = ch_versions.mix(SALMON_QUANT.out.versions.first())
 
+    SALMON_TX2GENE.config.publishDir = publish_dir
     SALMON_TX2GENE ( SALMON_QUANT.out.results.collect{it[1]}, gtf )
     ch_versions = ch_versions.mix(SALMON_TX2GENE.out.versions)
 
+    SALMON_TXIMPORT.config.publishDir = publish_dir
     SALMON_TXIMPORT ( SALMON_QUANT.out.results.collect{it[1]}, SALMON_TX2GENE.out.tsv.collect() )
     ch_versions = ch_versions.mix(SALMON_TXIMPORT.out.versions)
 
+    SALMON_SE_GENE.config.publishDir = publish_dir
     SALMON_SE_GENE (
         SALMON_TXIMPORT.out.counts_gene,
         SALMON_TXIMPORT.out.tpm_gene,
@@ -43,18 +59,21 @@ workflow QUANTIFY_SALMON {
     )
     ch_versions = ch_versions.mix(SALMON_SE_GENE.out.versions)
 
+    SALMON_SE_GENE_LENGTH_SCALED.config.publishDir = publish_dir
     SALMON_SE_GENE_LENGTH_SCALED (
         SALMON_TXIMPORT.out.counts_gene_length_scaled,
         SALMON_TXIMPORT.out.tpm_gene,
         SALMON_TX2GENE.out.tsv.collect()
     )
 
+    SALMON_SE_GENE_SCALED.config.publishDir = publish_dir
     SALMON_SE_GENE_SCALED (
         SALMON_TXIMPORT.out.counts_gene_scaled,
         SALMON_TXIMPORT.out.tpm_gene,
         SALMON_TX2GENE.out.tsv.collect()
     )
 
+    SALMON_SE_TRANSCRIPT.config.publishDir = publish_dir
     SALMON_SE_TRANSCRIPT (
         SALMON_TXIMPORT.out.counts_transcript,
         SALMON_TXIMPORT.out.tpm_transcript,
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
index 7c07084ff..33e569046 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
@@ -10,6 +10,11 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
     take:
     ch_bam_bai          // channel: [ val(meta), path(bam), path(bai/csi) ]
     val_get_dedup_stats // boolean: true/false
+    dedup_ext_prefix
+    index_ext_args
+    index_ext_prefix
+    index_publish_dir
+    stats_ext_prefix
 
     main:
 
@@ -18,12 +23,37 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
     //
     // UMI-tools dedup
     //
+    UMITOOLS_DEDUP.config.ext.args   = { [
+        meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
+        params.umitools_grouping_method ? "--method='${params.umitools_grouping_method}'" : '',
+        params.umitools_umi_separator   ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+    ].join(' ').trim() }
+    UMITOOLS_DEDUP.config.ext.prefix = dedup_ext_prefix
+    UMITOOLS_DEDUP.config.publishDir = [
+        [
+            path: "${params.outdir}/${params.aligner}/umitools",
+            mode: params.publish_dir_mode,
+            pattern: '*.tsv'
+        ],
+        [
+            path: "${params.outdir}/${params.aligner}",
+            mode: params.publish_dir_mode,
+            pattern: '*.bam',
+            enabled: (
+                params.save_align_intermeds ||
+                params.save_umi_intermeds
+            )
+        ]
+    ]
     UMITOOLS_DEDUP ( ch_bam_bai, val_get_dedup_stats )
     ch_versions = ch_versions.mix(UMITOOLS_DEDUP.out.versions.first())
 
     //
     // Index BAM file and run samtools stats, flagstat and idxstats
     //
+    SAMTOOLS_INDEX.config.ext.args   = index_ext_args
+    SAMTOOLS_INDEX.config.ext.prefix = index_ext_prefix
+    SAMTOOLS_INDEX.config.publishDir = index_publish_dir
     SAMTOOLS_INDEX ( UMITOOLS_DEDUP.out.bam )
     ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
@@ -39,6 +69,12 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
                 }
         }
 
+    BAM_STATS_SAMTOOLS.config.ext.prefix = stats_ext_prefix
+    BAM_STATS_SAMTOOLS.config.publishDir = [
+        path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
+        pattern: '*.{stats,flagstat,idxstats}'
+    ]
     BAM_STATS_SAMTOOLS ( ch_bam_bai_dedup, [ [:], [] ] )
     ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
 
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
index ee5960ed7..59255fe43 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf
+++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
@@ -56,7 +56,18 @@ workflow BAM_MARKDUPLICATES_PICARD {
                 }
         }
 
-    BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta )
+    samtools_ext_prefix = { "${meta.id}.markdup.sorted.bam" }
+    samtools_publish_dir = [
+        path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
+        pattern: '*.{stats,flagstat,idxstats}'
+    ]
+    BAM_STATS_SAMTOOLS (
+        ch_bam_bai,
+        ch_fasta,
+        samtools_ext_prefix,
+        samtools_publish_dir
+    )
     ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
 
     emit:
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
index fc1c652b9..c8ac28bab 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
@@ -10,14 +10,24 @@ workflow BAM_SORT_STATS_SAMTOOLS {
     take:
     ch_bam   // channel: [ val(meta), [ bam ] ]
     ch_fasta // channel: [ val(meta), path(fasta) ]
+    sort_ext_prefix
+    sort_publish_dir
+    index_ext_args
+    index_publish_dir
+    stats_ext_prefix
+    stats_publish_dir
 
     main:
 
     ch_versions = Channel.empty()
 
+    SAMTOOLS_SORT.config.ext.prefix = sort_ext_prefix
+    SAMTOOLS_SORT.config.publishDir = sort_publish_dir
     SAMTOOLS_SORT ( ch_bam )
     ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
 
+    SAMTOOLS_INDEX.config.ext.args   = index_ext_args
+    SAMTOOLS_INDEX.config.publishDir = index_publish_dir
     SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam )
     ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
 
@@ -34,7 +44,12 @@ workflow BAM_SORT_STATS_SAMTOOLS {
         }
         .set { ch_bam_bai }
 
-    BAM_STATS_SAMTOOLS ( ch_bam_bai, ch_fasta )
+    BAM_STATS_SAMTOOLS (
+        ch_bam_bai,
+        ch_fasta,
+        stats_ext_prefix,
+        stats_publish_dir
+    )
     ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)
 
     emit:
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index 44d4c010a..c95c56432 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -10,16 +10,24 @@ workflow BAM_STATS_SAMTOOLS {
     take:
     ch_bam_bai // channel: [ val(meta), path(bam), path(bai) ]
     ch_fasta   // channel: [ val(meta), path(fasta) ]
+    ext_prefix
+    publish_dir
 
     main:
     ch_versions = Channel.empty()
 
+    SAMTOOLS_STATS.config.ext.prefix = ext_prefix
+    SAMTOOLS_STATS.config.publishDir = publish_dir
     SAMTOOLS_STATS ( ch_bam_bai, ch_fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions)
 
+    SAMTOOLS_FLAGSTAT.config.ext.prefix = ext_prefix
+    SAMTOOLS_FLAGSTAT.config.publishDir = publish_dir
     SAMTOOLS_FLAGSTAT ( ch_bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)
 
+    SAMTOOLS_IDXSTATS.config.ext.prefix = ext_prefix
+    SAMTOOLS_IDXSTATS.config.publishDir = publish_dir
     SAMTOOLS_IDXSTATS ( ch_bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_IDXSTATS.out.versions)
 
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
index 6c3b7b0cb..fc7b9e262 100644
--- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
@@ -9,6 +9,8 @@ workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG {
     take:
     bedgraph // channel: [ val(meta), [ bedgraph ] ]
     sizes    //    path: chrom.sizes
+    clip_ext_prefix
+    bigwig_ext_prefix
 
     main:
 
@@ -17,12 +19,23 @@ workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG {
     //
     // Clip bedGraph file
     //
+    UCSC_BEDCLIP.config.ext.prefix = clip_ext_prefix
+    UCSC_BEDCLIP.config.publishDir = [
+        path: "${params.outdir}/${params.aligner}",
+        enabled: false
+    ]
     UCSC_BEDCLIP ( bedgraph, sizes )
     ch_versions = ch_versions.mix(UCSC_BEDCLIP.out.versions.first())
 
     //
     // Convert bedGraph to bigWig
     //
+    UCSC_BEDGRAPHTOBIGWIG.config.ext.prefix = bigwig_ext_prefix
+    UCSC_BEDGRAPHTOBIGWIG.config.publishDir = [
+        path: "${params.outdir}/${params.aligner}/bigwig",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+    ]
     UCSC_BEDGRAPHTOBIGWIG ( UCSC_BEDCLIP.out.bedgraph, sizes )
     ch_versions = ch_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions.first())
 
diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf
index 3be1dc0b3..fd4c8820c 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/main.nf
+++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf
@@ -43,7 +43,40 @@ workflow FASTQ_ALIGN_HISAT2 {
     //
     // Sort, index BAM file and run samtools stats, flagstat and idxstats
     //
-    BAM_SORT_STATS_SAMTOOLS ( HISAT2_ALIGN.out.bam, ch_fasta )
+    sort_ext_prefix = { "${meta.id}.sorted" }
+    sort_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.bam",
+        enabled: ( !params.with_umi && params.skip_markduplicates ) ||
+            params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    index_ext_args = params.bam_csi_index ? '-c' : ''
+    index_publish_dir = [
+        path: "${params.outdir}/${params.aligner}",
+        mode: params.publish_dir_mode,
+        pattern: "*.{bai,csi}",
+        enabled: ( !params.with_umi && params.skip_markduplicates ) ||
+            params.save_align_intermeds ||
+            params.skip_markduplicates
+    ]
+    stats_ext_prefix = { "${meta.id}.sorted.bam" }
+    stats_publish_dir = [
+        path: "${params.outdir}/${params.aligner}/samtools_stats",
+        mode: params.publish_dir_mode,
+        pattern: "*.{stats,flagstat,idxstats}"
+    ]
+    BAM_SORT_STATS_SAMTOOLS (
+        HISAT2_ALIGN.out.bam,
+        ch_fasta,
+        sort_ext_prefix,
+        sort_publish_dir,
+        index_ext_args,
+        index_publish_dir,
+        stats_ext_prefix,
+        stats_publish_dir
+    )
     ch_versions = ch_versions.mix(BAM_SORT_STATS_SAMTOOLS.out.versions)
 
 
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index b9e26e094..48bbd641d 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -447,9 +447,27 @@ workflow RNASEQ {
         //
         if (params.with_umi) {
             // Deduplicate genome BAM file before downstream analysis
+            dedup_ext_prefix  = { "${meta.id}.umi_dedup.sorted" }
+            index_ext_args    = params.bam_csi_index ? '-c' : ''
+            index_ext_prefix  = { "${meta.id}.umi_dedup.sorted" }
+            index_publish_dir = [
+                path: "${params.outdir}/${params.aligner}",
+                mode: params.publish_dir_mode,
+                pattern: '*.{bai,csi}',
+                enabled: (
+                    params.save_align_intermeds ||
+                    params.save_umi_intermeds
+                )
+            ]
+            stats_ext_prefix  = { "${meta.id}.umi_dedup.sorted.bam" }
             BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME (
                 ch_genome_bam.join(ch_genome_bam_index, by: [0]),
-                params.umitools_dedup_stats
+                params.umitools_dedup_stats,
+                dedup_ext_prefix,
+                index_ext_args,
+                index_ext_prefix,
+                index_publish_dir,
+                stats_ext_prefix
             )
             ch_genome_bam        = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bam
             ch_genome_bam_index  = BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.bai
@@ -462,17 +480,71 @@ workflow RNASEQ {
             ch_versions = ch_versions.mix(BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME.out.versions)
 
             // Co-ordinate sort, index and run stats on transcriptome BAM
+            sort_ext_prefix  = { "${meta.id}.transcriptome.sorted" }
+            sort_publish_dir = [
+                path: "${params.outdir}/${params.aligner}",
+                mode: params.publish_dir_mode,
+                pattern: '*.bam',
+                enabled: (
+                    params.save_align_intermeds ||
+                    params.save_umi_intermeds
+                )
+            ]
+            index_ext_args    = ''
+            index_publish_dir = [
+                path: "${params.outdir}/${params.aligner}",
+                mode: params.publish_dir_mode,
+                pattern: '*.bai',
+                enabled: (
+                    params.save_align_intermeds ||
+                    params.save_umi_intermeds
+                )
+            ]
+            stats_ext_prefix  = { "${meta.id}.transcriptome.sorted.bam" }
+            stats_publish_dir = [
+                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
+                )
+            ]
             BAM_SORT_STATS_SAMTOOLS (
                 ch_transcriptome_bam,
-                PREPARE_GENOME.out.fasta.map { [ [:], it ] }
+                PREPARE_GENOME.out.fasta.map { [ [:], it ] },
+                sort_ext_prefix,
+                sort_publish_dir,
+                index_ext_args,
+                index_publish_dir,
+                stats_ext_prefix,
+                stats_publish_dir
             )
             ch_transcriptome_sorted_bam = BAM_SORT_STATS_SAMTOOLS.out.bam
             ch_transcriptome_sorted_bai = BAM_SORT_STATS_SAMTOOLS.out.bai
 
             // Deduplicate transcriptome BAM file before read counting with Salmon
+            dedup_ext_prefix  = { "${meta.id}.umi_dedup.transcriptome.sorted" }
+            index_ext_args    = ''
+            index_ext_prefix  = ''
+            index_publish_dir = [
+                path: "${params.outdir}/${params.aligner}",
+                mode: params.publish_dir_mode,
+                pattern: '*.bai',
+                enabled: (
+                    params.save_align_intermeds ||
+                    params.save_umi_intermeds
+                )
+            ]
+            stats_ext_prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
             BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME (
                 ch_transcriptome_sorted_bam.join(ch_transcriptome_sorted_bai, by: [0]),
-                params.umitools_dedup_stats
+                params.umitools_dedup_stats,
+                dedup_ext_prefix,
+                index_ext_args,
+                index_ext_prefix,
+                index_publish_dir,
+                stats_ext_prefix
             )
 
             // Name sort BAM before passing to Salmon
@@ -543,7 +615,8 @@ workflow RNASEQ {
             PREPARE_GENOME.out.transcript_fasta,
             PREPARE_GENOME.out.gtf,
             true,
-            params.salmon_quant_libtype ?: ''
+            params.salmon_quant_libtype ?: '',
+            "${params.outdir}/${params.aligner}"
         )
         ch_versions = ch_versions.mix(QUANTIFY_STAR_SALMON.out.versions)
 
@@ -835,15 +908,23 @@ workflow RNASEQ {
         //
         // SUBWORKFLOW: Convert bedGraph to bigWig
         //
+        clip_ext_prefix = { "${meta.id}.clip.forward" }
+        bigwig_ext_prefix = { "${meta.id}.forward" }
         BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD (
             BEDTOOLS_GENOMECOV.out.bedgraph_forward,
-            PREPARE_GENOME.out.chrom_sizes
+            PREPARE_GENOME.out.chrom_sizes,
+            clip_ext_prefix,
+            bigwig_ext_prefix
         )
         ch_versions = ch_versions.mix(BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.versions)
 
+        clip_ext_prefix = { "${meta.id}.clip.reverse" }
+        bigwig_ext_prefix = { "${meta.id}.reverse" }
         BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE (
             BEDTOOLS_GENOMECOV.out.bedgraph_reverse,
-            PREPARE_GENOME.out.chrom_sizes
+            PREPARE_GENOME.out.chrom_sizes,
+            clip_ext_prefix,
+            bigwig_ext_prefix
         )
     }
 
@@ -968,7 +1049,8 @@ workflow RNASEQ {
             ch_dummy_file,
             PREPARE_GENOME.out.gtf,
             false,
-            params.salmon_quant_libtype ?: ''
+            params.salmon_quant_libtype ?: '',
+            "${params.outdir}/${params.pseudo_aligner}"
         )
         ch_salmon_multiqc = QUANTIFY_SALMON.out.results
         ch_versions = ch_versions.mix(QUANTIFY_SALMON.out.versions)