diff --git a/main.nf b/main.nf
index 59001a4f1..fe86d24f6 100755
--- a/main.nf
+++ b/main.nf
@@ -10,6 +10,7 @@
 */
 
 nextflow.enable.dsl = 2
+nextflow.preview.output = true
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/modules/local/bedtools_genomecov/nextflow.config b/modules/local/bedtools_genomecov/nextflow.config
index 85f3d34ae..f49fe8468 100644
--- a/modules/local/bedtools_genomecov/nextflow.config
+++ b/modules/local/bedtools_genomecov/nextflow.config
@@ -3,9 +3,6 @@ if (!params.skip_alignment && !params.skip_bigwig) {
     process {
         withName: 'BEDTOOLS_GENOMECOV' {
             ext.args   = '-split -du'
-            publishDir = [
-                enabled: false
-            ]
         }
     }
 }
diff --git a/modules/local/dupradar/nextflow.config b/modules/local/dupradar/nextflow.config
deleted file mode 100644
index 3ade56ad5..000000000
--- a/modules/local/dupradar/nextflow.config
+++ /dev/null
@@ -1,35 +0,0 @@
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_dupradar) {
-        process {
-            withName: 'DUPRADAR' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/scatter_plot" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Dens.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/box_plot" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Boxplot.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/histogram" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Hist.pdf"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/gene_data" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*Matrix.txt"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/dupradar/intercepts_slope" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*slope.txt"
-                    ]
-                ]
-            }
-        }
-    }
-}
diff --git a/modules/local/multiqc_custom_biotype/nextflow.config b/modules/local/multiqc_custom_biotype/nextflow.config
deleted file mode 100644
index 68fecaa66..000000000
--- a/modules/local/multiqc_custom_biotype/nextflow.config
+++ /dev/null
@@ -1,13 +0,0 @@
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
-        process {
-            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
diff --git a/modules/nf-core/bbmap/bbsplit/nextflow.config b/modules/nf-core/bbmap/bbsplit/nextflow.config
index da3ddaf31..0c37662da 100644
--- a/modules/nf-core/bbmap/bbsplit/nextflow.config
+++ b/modules/nf-core/bbmap/bbsplit/nextflow.config
@@ -2,19 +2,6 @@ if (!params.skip_bbsplit) {
     process {
         withName: 'BBMAP_BBSPLIT' {
             ext.args   = 'build=1 ambiguous2=all maxindel=150000'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/bbsplit" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.txt'
-                ],
-                [
-                    path: { params.save_bbsplit_reads ? "${params.outdir}/bbsplit" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_bbsplit_reads ? it : null }
-                ]
-            ]
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/cat/fastq/nextflow.config b/modules/nf-core/cat/fastq/nextflow.config
deleted file mode 100644
index 64de2e49c..000000000
--- a/modules/nf-core/cat/fastq/nextflow.config
+++ /dev/null
@@ -1,9 +0,0 @@
-process {
-    withName: 'CAT_FASTQ' {
-        publishDir = [
-            path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
-        ]
-    }
-}
diff --git a/modules/nf-core/multiqc/nextflow.config b/modules/nf-core/multiqc/nextflow.config
index ac178787c..0f1fffdda 100644
--- a/modules/nf-core/multiqc/nextflow.config
+++ b/modules/nf-core/multiqc/nextflow.config
@@ -3,14 +3,6 @@ if (!params.skip_multiqc) {
         withName: 'MULTIQC' {
             ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
             ext.prefix = "multiqc_report"
-            publishDir = [
-                path: { [
-                    "${params.outdir}/multiqc",
-                    params.skip_alignment? '' : "/${params.aligner}"
-                    ].join('') },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/modules/nf-core/preseq/lcextrap/nextflow.config
index e203e87e7..fdb888749 100644
--- a/modules/nf-core/preseq/lcextrap/nextflow.config
+++ b/modules/nf-core/preseq/lcextrap/nextflow.config
@@ -3,18 +3,6 @@ if (!params.skip_alignment && !params.skip_qc) {
         process {
             withName: 'PRESEQ_LCEXTRAP' {
                 ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/preseq" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.txt"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/preseq/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.log"
-                    ]
-                ]
             }
         }
     }
diff --git a/modules/nf-core/qualimap/rnaseq/nextflow.config b/modules/nf-core/qualimap/rnaseq/nextflow.config
deleted file mode 100644
index 9c05fb25a..000000000
--- a/modules/nf-core/qualimap/rnaseq/nextflow.config
+++ /dev/null
@@ -1,13 +0,0 @@
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_qualimap) {
-        process {
-            withName: 'QUALIMAP_RNASEQ' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/qualimap" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
diff --git a/modules/nf-core/sortmerna/nextflow.config b/modules/nf-core/sortmerna/nextflow.config
index 8771660ce..2f60c9b7b 100644
--- a/modules/nf-core/sortmerna/nextflow.config
+++ b/modules/nf-core/sortmerna/nextflow.config
@@ -2,19 +2,6 @@ if (params.remove_ribo_rna) {
     process {
         withName: 'SORTMERNA' {
             ext.args   = '--num_alignments 1 -v'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/sortmerna" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { params.save_non_ribo_reads ? "${params.outdir}/sortmerna" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    saveAs: { params.save_non_ribo_reads ? it : null }
-                ]
-            ]
         }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/stringtie/stringtie/nextflow.config b/modules/nf-core/stringtie/stringtie/nextflow.config
index dc0651458..03518ca96 100644
--- a/modules/nf-core/stringtie/stringtie/nextflow.config
+++ b/modules/nf-core/stringtie/stringtie/nextflow.config
@@ -6,11 +6,6 @@ if (!params.skip_alignment) {
                     '-v',
                     params.stringtie_ignore_gtf ? '' : '-e'
                 ].join(' ').trim() }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/stringtie" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
             }
         }
     }
diff --git a/modules/nf-core/subread/featurecounts/nextflow.config b/modules/nf-core/subread/featurecounts/nextflow.config
index 3a796d101..c75038ca9 100644
--- a/modules/nf-core/subread/featurecounts/nextflow.config
+++ b/modules/nf-core/subread/featurecounts/nextflow.config
@@ -7,19 +7,6 @@ if (!params.skip_alignment && !params.skip_qc) {
                     params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
                     "-t $params.featurecounts_feature_type"
                 ].join(' ').trim() }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-
-            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
             }
         }
     }
diff --git a/nextflow.config b/nextflow.config
index 74108e825..9664eabdf 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -135,14 +135,8 @@ params {
 
 }
 
-// Default publishing logic for pipeline
-process {
-    publishDir = [
-        path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
-        mode: params.publish_dir_mode,
-        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-    ]
-}
+outputDir = params.outdir
+workflow.output.mode = params.publish_dir_mode
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
diff --git a/subworkflows/local/align_star/main.nf b/subworkflows/local/align_star/main.nf
index 4f516e8e0..a3c6c52db 100644
--- a/subworkflows/local/align_star/main.nf
+++ b/subworkflows/local/align_star/main.nf
@@ -80,4 +80,14 @@ workflow ALIGN_STAR {
     idxstats       = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
     versions       = ch_versions                    // channel: [ versions.yml ]
+
+    publish:
+    ch_orig_bam         >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    ch_log_final        >> 'star_salmon/log'
+    ch_log_out          >> 'star_salmon/log'
+    ch_log_progress     >> 'star_salmon/log'
+    ch_bam_sorted       >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    ch_bam_transcript   >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    ch_fastq            >> (params.save_unaligned ? 'star_salmon/unmapped' : null)
+    ch_tab              >> 'star_salmon/log'
 }
diff --git a/subworkflows/local/align_star/nextflow.config b/subworkflows/local/align_star/nextflow.config
index 68bfef562..beeadc15a 100644
--- a/subworkflows/local/align_star/nextflow.config
+++ b/subworkflows/local/align_star/nextflow.config
@@ -15,25 +15,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                 params.save_unaligned ? '--outReadsUnmapped Fastx' : '',
                 params.extra_star_align_args ? params.extra_star_align_args.split("\\s(?=--)") : ''
             ].flatten().unique(false).join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{out,tab}'
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_unaligned ? it : null }
-                ]
-            ]
         }
     }
 }
diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf
index 58a9b293c..701630d9d 100644
--- a/subworkflows/local/prepare_genome/main.nf
+++ b/subworkflows/local/prepare_genome/main.nf
@@ -76,6 +76,7 @@ workflow PREPARE_GENOME {
     //
     if (gtf || gff) {
         if (gtf) {
+            ch_gff = Channel.empty()
             if (gtf.endsWith('.gz')) {
                 ch_gtf      = GUNZIP_GTF ( [ [:], gtf ] ).gunzip.map { it[1] }
                 ch_versions = ch_versions.mix(GUNZIP_GTF.out.versions)
@@ -327,6 +328,30 @@ workflow PREPARE_GENOME {
         }
     }
 
+    //
+    // Collect channels for publishing
+    //
+    ch_genome = Channel.empty().mix(
+        ch_fasta,
+        ch_gtf,
+        ch_gff,
+        ch_add_fasta,
+        ch_gene_bed,
+        ch_transcript_fasta,
+        ch_fai,
+        ch_chrom_sizes,
+    )
+
+    ch_genome_index = Channel.empty().mix(
+        ch_splicesites,
+        ch_bbsplit_index,
+        ch_star_index,
+        ch_rsem_index,
+        ch_hisat2_index,
+        ch_salmon_index,
+        ch_kallisto_index,
+    )
+
     emit:
     fasta            = ch_fasta                  // channel: path(genome.fasta)
     gtf              = ch_gtf                    // channel: path(genome.gtf)
@@ -342,4 +367,8 @@ workflow PREPARE_GENOME {
     salmon_index     = ch_salmon_index           // channel: path(salmon/index/)
     kallisto_index   = ch_kallisto_index         // channel: [ meta, path(kallisto/index/) ]
     versions         = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+
+    publish:
+    ch_genome       >> (params.save_reference ? 'genome' : null)
+    ch_genome_index >> (params.save_reference ? 'genome/index' : null)
 }
diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config
index 98a4b64fd..62d84f340 100644
--- a/subworkflows/local/prepare_genome/nextflow.config
+++ b/subworkflows/local/prepare_genome/nextflow.config
@@ -1,39 +1,10 @@
 process {
-    withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
     withName: 'UNTAR_.*' {
         ext.args2 = '--no-same-owner'
     }
 
-    withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'HISAT2_EXTRACTSPLICESITES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'SALMON_INDEX' {
@@ -41,62 +12,18 @@ process {
                 params.gencode ? '--gencode' : '',
                 params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
         ].join(' ').trim() }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'KALLISTO_INDEX' {
         ext.args   = params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}" : ''
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'RSEM_PREPAREREFERENCE_GENOME' {
         ext.args   = '--star'
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'GTF2BED' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CAT_ADDITIONAL_FASTA|PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 
     withName: 'GTF_FILTER' {
         ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
-    }
-
-    withName: 'CUSTOM_GETCHROMSIZES' {
-        publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-        ]
     }
 }
 
@@ -104,11 +31,6 @@ if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
     process {
         withName: 'PREPARE_GENOME:BBMAP_BBSPLIT' {
             ext.args   = 'build=1'
-            publishDir = [
-                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-            ]
         }
     }
 }
diff --git a/subworkflows/local/quantify_rsem/main.nf b/subworkflows/local/quantify_rsem/main.nf
index 4b7473634..577b76589 100644
--- a/subworkflows/local/quantify_rsem/main.nf
+++ b/subworkflows/local/quantify_rsem/main.nf
@@ -59,4 +59,15 @@ workflow QUANTIFY_RSEM {
     merged_tpm_transcript    = RSEM_MERGE_COUNTS.out.tpm_transcript           //    path: *.transcript_tpm.tsv
 
     versions                 = ch_versions                                    // channel: [ versions.yml ]
+
+    publish:
+    RSEM_CALCULATEEXPRESSION.out.counts_gene        >> 'star_rsem'
+    RSEM_CALCULATEEXPRESSION.out.counts_transcript  >> 'star_rsem'
+    RSEM_CALCULATEEXPRESSION.out.stat               >> 'star_rsem'
+    RSEM_CALCULATEEXPRESSION.out.logs               >> 'star_rsem/log'
+    RSEM_CALCULATEEXPRESSION.out.bam_star           >> (params.save_align_intermeds ? 'star_rsem' : null)
+    RSEM_CALCULATEEXPRESSION.out.bam_genome         >> (params.save_align_intermeds ? 'star_rsem' : null)
+    RSEM_CALCULATEEXPRESSION.out.bam_transcript     >> (params.save_align_intermeds ? 'star_rsem' : null)
+    RSEM_MERGE_COUNTS.out           >> 'star_rsem'
+    RSEM_MERGE_COUNTS.out.versions  >> null
 }
diff --git a/subworkflows/local/quantify_rsem/nextflow.config b/subworkflows/local/quantify_rsem/nextflow.config
index 7b50b86c0..5a03a5576 100644
--- a/subworkflows/local/quantify_rsem/nextflow.config
+++ b/subworkflows/local/quantify_rsem/nextflow.config
@@ -8,32 +8,6 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
                 '--estimate-rspd',
                 '--seed 1'
             ].join(' ').trim()
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.{stat,results}"
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.bam",
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ]
-            ]
-        }
-
-        withName: '.*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
         }
     }
 }
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..783332f2f 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
@@ -52,4 +52,13 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
     idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), path(idxstats) ]
 
     versions = ch_versions                     // channel: [ path(versions.yml) ]
+
+    publish:
+    UMITOOLS_DEDUP.out.bam                  >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    UMITOOLS_DEDUP.out.tsv_edit_distance    >> 'star_salmon/umitools'
+    UMITOOLS_DEDUP.out.tsv_per_umi          >> 'star_salmon/umitools'
+    UMITOOLS_DEDUP.out.tsv_umi_per_position >> 'star_salmon/umitools'
+    SAMTOOLS_INDEX.out.bai                  >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    BAM_STATS_SAMTOOLS.out                  >> 'star_salmon/samtools_stats'
+    BAM_STATS_SAMTOOLS.out.versions         >> null
 }
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/main.nf b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
index de8130fb5..ca7bbe674 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/main.nf
+++ b/subworkflows/nf-core/bam_markduplicates_picard/main.nf
@@ -46,3 +46,21 @@ workflow BAM_MARKDUPLICATES_PICARD {
 
     versions = ch_versions                       // channel: [ versions.yml ]
 }
+
+workflow {
+    main:
+    def ch_bam = Channel.empty()
+    def ch_fasta = Channel.empty()
+    def ch_fai = Channel.empty()
+
+    BAM_MARKDUPLICATES_PICARD( ch_bam, ch_fasta, ch_fai )
+
+    publish:
+    BAM_MARKDUPLICATES_PICARD.out.bam       >> 'picard'
+    BAM_MARKDUPLICATES_PICARD.out.metrics   >> 'picard/metrics'
+    BAM_MARKDUPLICATES_PICARD.out.bai       >> 'picard'
+    BAM_MARKDUPLICATES_PICARD.out.csi       >> 'picard'
+    BAM_MARKDUPLICATES_PICARD.out.stats     >> 'picard/samtools_stats'
+    BAM_MARKDUPLICATES_PICARD.out.flagstat  >> 'picard/samtools_stats'
+    BAM_MARKDUPLICATES_PICARD.out.idxstats  >> 'picard/samtools_stats'
+}
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
index 2778db78d..f8f3061e7 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
+++ b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
@@ -4,37 +4,15 @@ if (!params.skip_alignment) {
             withName: '.*:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
                 ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
                 ext.prefix = { "${meta.id}.markdup.sorted" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/picard_metrics" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*metrics.txt'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam'
-                    ]
-                ]
             }
 
             withName: '.*:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
                 ext.args   = { params.bam_csi_index ? '-c' : '' }
                 ext.prefix = { "${meta.id}.markdup.sorted" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}'
-                ]
             }
 
             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}'
-                ]
             }
         }
     }
diff --git a/subworkflows/nf-core/bam_rseqc/main.nf b/subworkflows/nf-core/bam_rseqc/main.nf
index 043321a13..de674f2a9 100644
--- a/subworkflows/nf-core/bam_rseqc/main.nf
+++ b/subworkflows/nf-core/bam_rseqc/main.nf
@@ -183,3 +183,35 @@ workflow BAM_RSEQC {
 
     versions                        // channel: [ versions.yml ]
 }
+
+workflow {
+    main:
+    def bam_bai = Channel.empty()
+    def bed = Channel.empty()
+    def rseqc_modules = Channel.empty()
+    BAM_RSEQC(bam_bai, bed, rseqc_modules)
+
+    publish:
+    BAM_RSEQC.out.bamstat_txt                     >> 'rseqc/bam_stat'
+    BAM_RSEQC.out.inferexperiment_txt             >> 'rseqc/infer_experiment'
+    BAM_RSEQC.out.junctionannotation_pdf          >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_events_pdf   >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_bed          >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_interact_bed >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_xls          >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_log          >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionannotation_rscript      >> 'rseqc/junction_annotation'
+    BAM_RSEQC.out.junctionsaturation_pdf          >> 'rseqc/junction_saturation'
+    BAM_RSEQC.out.junctionsaturation_rscript      >> 'rseqc/junction_saturation'
+    BAM_RSEQC.out.readduplication_pdf             >> 'rseqc/read_duplication'
+    BAM_RSEQC.out.readduplication_seq_xls         >> 'rseqc/read_duplication'
+    BAM_RSEQC.out.readduplication_pos_xls         >> 'rseqc/read_duplication'
+    BAM_RSEQC.out.readduplication_rscript         >> 'rseqc/read_duplication'
+    BAM_RSEQC.out.readdistribution_txt            >> 'rseqc/read_distribution'
+    BAM_RSEQC.out.innerdistance_distance          >> 'rseqc/inner_distance'
+    BAM_RSEQC.out.innerdistance_freq              >> 'rseqc/inner_distance'
+    BAM_RSEQC.out.innerdistance_mean              >> 'rseqc/inner_distance'
+    BAM_RSEQC.out.innerdistance_pdf               >> 'rseqc/inner_distance'
+    BAM_RSEQC.out.innerdistance_rscript           >> 'rseqc/inner_distance'
+    BAM_RSEQC.out.tin_txt                         >> 'rseqc/tin'
+}
diff --git a/subworkflows/nf-core/bam_rseqc/nextflow.config b/subworkflows/nf-core/bam_rseqc/nextflow.config
deleted file mode 100644
index 4fabc8e99..000000000
--- a/subworkflows/nf-core/bam_rseqc/nextflow.config
+++ /dev/null
@@ -1,153 +0,0 @@
-def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []
-
-if (!params.skip_alignment && !params.skip_qc && !params.skip_rseqc) {
-    if ('bam_stat' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_BAMSTAT' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/bam_stat" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if ('infer_experiment' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/infer_experiment" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if ('junction_annotation' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/bed" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bed'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/xls" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.xls'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.log'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_annotation/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if ('junction_saturation' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/junction_saturation/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if ('read_duplication' in rseqc_modules) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_READDUPLICATION' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/xls" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.xls'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/read_duplication/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if ('read_distribution' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/read_distribution" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-
-    if ('inner_distance' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_INNERDISTANCE' {
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/txt" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.txt',
-                        saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/pdf" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.pdf'
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.aligner}/rseqc/inner_distance/rscript" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.r'
-                    ]
-                ]
-            }
-        }
-    }
-
-    if ('tin' in rseqc_modules && !params.bam_csi_index) {
-        process {
-            withName: '.*:BAM_RSEQC:RSEQC_TIN' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/rseqc/tin" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
index 6c3b7b0cb..688db1f6b 100644
--- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
+++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/main.nf
@@ -32,3 +32,13 @@ workflow BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG {
 
     versions = ch_versions                      // channel: [ versions.yml ]
 }
+
+workflow {
+    main:
+    def bedgraph = Channel.empty()
+    def sizes = Channel.empty()
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG(bedgraph, sizes)
+
+    publish:
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG.out.bigwig >> 'bigwig'
+}
diff --git a/subworkflows/nf-core/fastq_align_hisat2/main.nf b/subworkflows/nf-core/fastq_align_hisat2/main.nf
index a2ec1cf5e..554be9432 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/main.nf
+++ b/subworkflows/nf-core/fastq_align_hisat2/main.nf
@@ -40,5 +40,10 @@ workflow FASTQ_ALIGN_HISAT2 {
     idxstats = BAM_SORT_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
 
     versions = ch_versions                          // channel: [ versions.yml ]
+
+    publish:
+    HISAT2_ALIGN.out.bam        >> (params.save_align_intermeds ? 'hisat2' : null)
+    HISAT2_ALIGN.out.summary    >> 'hisat2/log'
+    HISAT2_ALIGN.out.fastq      >> (params.save_unaligned ? 'hisat2/unmapped' : null)
 }
 
diff --git a/subworkflows/nf-core/fastq_align_hisat2/nextflow.config b/subworkflows/nf-core/fastq_align_hisat2/nextflow.config
index 0f6d1abdc..f358884a5 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/nextflow.config
+++ b/subworkflows/nf-core/fastq_align_hisat2/nextflow.config
@@ -2,25 +2,6 @@ if (!params.skip_alignment && params.aligner == 'hisat2') {
     process {
         withName: '.*:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN' {
             ext.args   = '--met-stderr --new-summary --dta'
-            publishDir = [
-                [
-                    path: { "${params.outdir}/${params.aligner}/log" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.log'
-                ],
-                [
-                    path: { params.save_align_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds ? it : null }
-                ],
-                [
-                    path: { params.save_unaligned ? "${params.outdir}/${params.aligner}/unmapped" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.fastq.gz',
-                    saveAs: { params.save_unaligned ? it : null }
-                ]
-            ]
         }
     }
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
index 764ce013f..966bdaa6a 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf
@@ -154,4 +154,17 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP {
     fastqc_trim_zip    // channel: [ val(meta), [ zip ] ]
 
     versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+
+    publish:
+    // TODO: need to recover trim_reads and umi_reads
+    // trim_reads          >> (params.save_trimmed ? 'fastp/intermeds' : null)
+    // umi_reads           >> (params.save_umi_intermeds ? 'umitools' : null)
+    umi_log             >> 'umitools'
+    trim_json           >> 'fastp'
+    trim_html           >> 'fastp'
+    trim_log            >> 'fastp/log'
+    trim_reads_fail     >> (params.save_trimmed ? 'fastp/intermeds' : null)
+    trim_reads_merged   >> (params.save_trimmed ? 'fastp/intermeds' : null)
+    fastqc_trim_html    >> 'fastp/fastqc'
+    fastqc_trim_zip     >> 'fastp/fastqc'
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
index 061689d5f..e17897297 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
@@ -7,11 +7,6 @@ if (!(params.skip_fastqc || params.skip_qc)) {
 
             withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
                 ext.args   = '--quiet'
-                publishDir = [
-                    path: { "${params.outdir}/${params.trimmer}/fastqc" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
             }
         }
     }
@@ -22,24 +17,6 @@ if (!params.skip_trimming) {
         process {
             withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
                 ext.args   = { params.extra_fastp_args ?: '' }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.trimmer}" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.{json,html}"
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.trimmer}/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.log"
-                    ],
-                    [
-                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.fastq.gz",
-                        saveAs: { params.save_trimmed ? it : null }
-                    ]
-                ]
             }
         }
     }
@@ -54,19 +31,6 @@ if (params.with_umi && !params.skip_umi_extract) {
                     params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
                     params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
             ].join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    saveAs: { params.save_umi_intermeds ? it : null }
-                ]
-            ]
         }
     }
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
index db2e5b329..fc257f969 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf
@@ -120,4 +120,13 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE {
     trim_read_count    // channel: [ val(meta), val(count) ]
 
     versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
+
+    publish:
+    // TODO: need to recover trim_reads and umi_reads
+    // trim_reads >> (params.save_trimmed ? 'trimgalore' : null)
+    // umi_reads  >> (params.save_umi_intermeds ? 'umitools' : null)
+    umi_log    >> 'umitools'
+    trim_html  >> 'trimgalore/fastqc'
+    trim_zip   >> 'trimgalore/fastqc'
+    trim_log   >> 'trimgalore'
 }
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
index 7279111e5..48181b085 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config
@@ -18,24 +18,6 @@ if (!params.skip_trimming) {
                         params.extra_trimgalore_args ? params.extra_trimgalore_args.split("\\s(?=--)") : ''
                     ].flatten().unique(false).join(' ').trim()
                 }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.trimmer}/fastqc" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.{html,zip}"
-                    ],
-                    [
-                        path: { params.save_trimmed ? "${params.outdir}/${params.trimmer}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.fq.gz",
-                        saveAs: { params.save_trimmed ? it : null }
-                    ],
-                    [
-                        path: { "${params.outdir}/${params.trimmer}" },
-                        mode: params.publish_dir_mode,
-                        pattern: "*.txt"
-                    ]
-                ]
             }
         }
     }
@@ -50,19 +32,6 @@ if (params.with_umi && !params.skip_umi_extract) {
                     params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
                     params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
             ].join(' ').trim() }
-            publishDir = [
-                [
-                    path: { "${params.outdir}/umitools" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.log"
-                ],
-                [
-                    path: { params.save_umi_intermeds ? "${params.outdir}/umitools" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz",
-                    saveAs: { params.save_umi_intermeds ? it : null }
-                ]
-            ]
         }
     }
 }
diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config b/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
index 36a8c5d7a..685b68bd5 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
@@ -2,15 +2,9 @@ process {
     withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE' {
         ext.args   = '--record-count 1000000 --seed 1'
         ext.prefix = { "${meta.id}.subsampled" }
-        publishDir = [
-            enabled: false
-        ]
     }
 
     withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
         ext.args   = '--skipQuant'
-        publishDir = [
-            enabled: false
-        ]
     }
 }
diff --git a/workflows/rnaseq/main.nf b/workflows/rnaseq/main.nf
index 5c7c2b964..6a80cc6d0 100755
--- a/workflows/rnaseq/main.nf
+++ b/workflows/rnaseq/main.nf
@@ -785,6 +785,105 @@ workflow RNASEQ {
     emit:
     multiqc_report = ch_multiqc_report // channel: /path/to/multiqc_report.html
     versions       = ch_versions       // channel: [ path(versions.yml) ]
+
+    publish:
+    QUANTIFY_STAR_SALMON.out                            >> 'star_salmon'
+    QUANTIFY_STAR_SALMON.out.multiqc                    >> null
+    QUANTIFY_STAR_SALMON.out.merged_counts_transcript   >> null
+    QUANTIFY_STAR_SALMON.out.merged_tpm_transcript      >> null
+    QUANTIFY_STAR_SALMON.out.versions                   >> null
+
+    // TODO: !params.skip_alignment && params.aligner == 'star_salmon' && params.with_umi
+    // BAM_SORT_STATS_SAMTOOLS.out.bam         >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    // BAM_SORT_STATS_SAMTOOLS.out.bai         >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    // BAM_SORT_STATS_SAMTOOLS.out.stats       >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/samtools_stats' : null)
+    // BAM_SORT_STATS_SAMTOOLS.out.flagstat    >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/samtools_stats' : null)
+    // BAM_SORT_STATS_SAMTOOLS.out.idxstats    >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/samtools_stats' : null)
+    // SAMTOOLS_SORT.out.bam                   >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    // UMITOOLS_PREPAREFORSALMON.out.bam       >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon' : null)
+    // UMITOOLS_PREPAREFORSALMON.out.log       >> (params.save_align_intermeds || params.save_umi_intermeds ? 'star_salmon/umitools/log' : null)
+
+    // TODO: !params.skip_alignment && params.aligner == 'star_salmon'
+    DESEQ2_QC_STAR_SALMON.out               >> 'star_salmon/deseq2_qc'
+    DESEQ2_QC_STAR_SALMON.out.pca_multiqc   >> null
+    DESEQ2_QC_STAR_SALMON.out.dists_multiqc >> null
+    DESEQ2_QC_STAR_SALMON.out.versions      >> null
+
+    // TODO: !params.skip_alignment && params.aligner == 'star_rsem'
+    // DESEQ2_QC_RSEM.out               >> 'star_rsem/deseq2_qc'
+    // DESEQ2_QC_RSEM.out.pca_multiqc   >> null
+    // DESEQ2_QC_RSEM.out.dists_multiqc >> null
+    // DESEQ2_QC_RSEM.out.versions      >> null
+
+    QUANTIFY_PSEUDO_ALIGNMENT.out                           >> params.pseudo_aligner
+    QUANTIFY_PSEUDO_ALIGNMENT.out.results                   >> null
+    QUANTIFY_PSEUDO_ALIGNMENT.out.multiqc                   >> null
+    QUANTIFY_PSEUDO_ALIGNMENT.out.merged_counts_transcript  >> null
+    QUANTIFY_PSEUDO_ALIGNMENT.out.merged_tpm_transcript     >> null
+    QUANTIFY_PSEUDO_ALIGNMENT.out.versions                  >> null
+    // TODO: process 'QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE'
+
+    DESEQ2_QC_PSEUDO.out                >> "${params.pseudo_aligner}/deseq2_qc"
+    DESEQ2_QC_PSEUDO.out.pca_multiqc    >> null
+    DESEQ2_QC_PSEUDO.out.dists_multiqc  >> null
+    DESEQ2_QC_PSEUDO.out.versions       >> null
+
+    BBMAP_BBSPLIT.out.stats     >> 'bbsplit'
+    BBMAP_BBSPLIT.out.all_fastq >> (params.save_bbsplit_reads ? 'bbsplit' : null)
+    CAT_FASTQ.out.reads         >> (params.save_merged_fastq ? 'fastq' : null)
+
+    // TODO: params.remove_ribo_rna
+    // SORTMERNA.out.reads         >> (params.save_non_ribo_reads ? 'sortmerna' : null)
+
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD.out.bigwig >> "${params.aligner}/bigwig"
+    BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE.out.bigwig >> "${params.aligner}/bigwig"
+    DUPRADAR.out.pdf                >> "${params.aligner}/dupradar"
+    DUPRADAR.out.txt                >> "${params.aligner}/dupradar"
+    MULTIQC.out.report              >> (params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}")
+    MULTIQC.out.data                >> (params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}")
+    MULTIQC.out.plots               >> (params.skip_alignment ? 'multiqc' : "multiqc/${params.aligner}")
+
+    // TODO: !params.skip_alignment && !params.skip_qc && !params.skip_preseq
+    // PRESEQ_LCEXTRAP.out.lc_extrap   >> "${params.aligner}/preseq"
+    // PRESEQ_LCEXTRAP.out.log         >> "${params.aligner}/preseq/log"
+
+    QUALIMAP_RNASEQ.out.results         >> "${params.aligner}/qualimap"
+    STRINGTIE_STRINGTIE.out             >> "${params.aligner}/stringtie"
+    STRINGTIE_STRINGTIE.out.versions    >> null
+    MULTIQC_CUSTOM_BIOTYPE.out.tsv      >> "${params.aligner}/featurecounts"
+    SUBREAD_FEATURECOUNTS.out           >> "${params.aligner}/featurecounts"
+    SUBREAD_FEATURECOUNTS.out.versions  >> null
+
+    BAM_MARKDUPLICATES_PICARD.out.bam       >> "${params.aligner}"
+    BAM_MARKDUPLICATES_PICARD.out.bai       >> "${params.aligner}"
+    BAM_MARKDUPLICATES_PICARD.out.csi       >> "${params.aligner}"
+    BAM_MARKDUPLICATES_PICARD.out.metrics   >> "${params.aligner}/picard_metrics"
+    BAM_MARKDUPLICATES_PICARD.out.stats     >> "${params.aligner}/samtools_stats"
+    BAM_MARKDUPLICATES_PICARD.out.flagstat  >> "${params.aligner}/samtools_stats"
+    BAM_MARKDUPLICATES_PICARD.out.idxstats  >> "${params.aligner}/samtools_stats"
+
+    BAM_RSEQC.out.bamstat_txt                       >> "${params.aligner}/rseqc/bam_stat"
+    BAM_RSEQC.out.inferexperiment_txt               >> "${params.aligner}/rseqc/infer_experiment"
+    BAM_RSEQC.out.junctionannotation_pdf            >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_events_pdf     >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_bed            >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_interact_bed   >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_xls            >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_log            >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionannotation_rscript        >> "${params.aligner}/rseqc/junction_annotation"
+    BAM_RSEQC.out.junctionsaturation_pdf            >> "${params.aligner}/rseqc/junction_saturation"
+    BAM_RSEQC.out.junctionsaturation_rscript        >> "${params.aligner}/rseqc/junction_saturation"
+    BAM_RSEQC.out.readduplication_pdf               >> "${params.aligner}/rseqc/read_duplication"
+    BAM_RSEQC.out.readduplication_seq_xls           >> "${params.aligner}/rseqc/read_duplication"
+    BAM_RSEQC.out.readduplication_pos_xls           >> "${params.aligner}/rseqc/read_duplication"
+    BAM_RSEQC.out.readduplication_rscript           >> "${params.aligner}/rseqc/read_duplication"
+    BAM_RSEQC.out.readdistribution_txt              >> "${params.aligner}/rseqc/read_distribution"
+    BAM_RSEQC.out.innerdistance_distance            >> "${params.aligner}/rseqc/inner_distance"
+    BAM_RSEQC.out.innerdistance_freq                >> "${params.aligner}/rseqc/inner_distance"
+    BAM_RSEQC.out.innerdistance_mean                >> "${params.aligner}/rseqc/inner_distance"
+    BAM_RSEQC.out.innerdistance_pdf                 >> "${params.aligner}/rseqc/inner_distance"
+    BAM_RSEQC.out.innerdistance_rscript             >> "${params.aligner}/rseqc/inner_distance"
+    BAM_RSEQC.out.tin_txt                           >> "${params.aligner}/rseqc/tin"
 }
 
 /*
diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
index f988d3d7c..487c172b6 100644
--- a/workflows/rnaseq/nextflow.config
+++ b/workflows/rnaseq/nextflow.config
@@ -1,18 +1,13 @@
 includeConfig "../../modules/local/bedtools_genomecov/nextflow.config"
-includeConfig "../../modules/local/dupradar/nextflow.config"
-includeConfig "../../modules/local/multiqc_custom_biotype/nextflow.config"
 includeConfig "../../modules/nf-core/bbmap/bbsplit/nextflow.config"
-includeConfig "../../modules/nf-core/cat/fastq/nextflow.config"
 includeConfig "../../modules/nf-core/multiqc/nextflow.config"
 includeConfig "../../modules/nf-core/preseq/lcextrap/nextflow.config"
-includeConfig "../../modules/nf-core/qualimap/rnaseq/nextflow.config"
 includeConfig "../../modules/nf-core/sortmerna/nextflow.config"
 includeConfig "../../modules/nf-core/stringtie/stringtie/nextflow.config"
 includeConfig "../../modules/nf-core/subread/featurecounts/nextflow.config"
 includeConfig "../../subworkflows/local/align_star/nextflow.config"
 includeConfig "../../subworkflows/local/quantify_rsem/nextflow.config"
 includeConfig "../../subworkflows/nf-core/bam_markduplicates_picard/nextflow.config"
-includeConfig "../../subworkflows/nf-core/bam_rseqc/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_align_hisat2/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config"
 includeConfig "../../subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/nextflow.config"
@@ -26,37 +21,12 @@ 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:CUSTOM_TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
         withName: '.*:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT' {
             ext.prefix = { "${quant_type}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
         }
-
         withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
             ext.prefix = { "${params.pseudo_aligner}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
-            ]
         }
         withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE' {
             ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
@@ -77,58 +47,18 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
             withName: 'NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT' {
                 ext.args   = '-n'
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:UMITOOLS_PREPAREFORSALMON' {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.filtered" }
-                publishDir = [
-                    [
-                        path: { "${params.outdir}/${params.aligner}/umitools/log" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.log'
-                    ],
-                    [
-                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                    ]
-                ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bam',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
-            }
-
-            withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
             }
 
             withName: 'NFCORE_RNASEQ:RNASEQ:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.transcriptome.sorted.bam" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}/samtools_stats" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
@@ -138,37 +68,10 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     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.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                    ]
-                ]
-            }
-
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX' {
-                publishDir = [
-                    path: { params.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.bai',
-                    saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
-                ]
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.umi_dedup.transcriptome.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
             }
         }
     }
@@ -182,39 +85,14 @@ if (!params.skip_alignment) {
     process {
         withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:.*' {
             ext.prefix = { "${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 = { "${meta.id}.sorted" }
-            publishDir = [
-                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
-                mode: params.publish_dir_mode,
-                pattern: "*.bam",
-                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' : '' }
-            publishDir = [
-                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
-                mode: params.publish_dir_mode,
-                pattern: "*.{bai,csi}",
-                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 }
-            ]
         }
     }
 
@@ -227,39 +105,15 @@ if (!params.skip_alignment) {
                     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.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam',
-                        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.prefix = { "${meta.id}.umi_dedup.sorted" }
-                publishDir = [
-                    path: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}',
-                    saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
-                ]
             }
 
             withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*' {
                 ext.prefix = { "${meta.id}.umi_dedup.sorted.bam" }
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
             }
         }
     }
@@ -273,34 +127,18 @@ if (!params.skip_alignment && !params.skip_bigwig) {
     process {
         withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
             ext.prefix = { "${meta.id}.clip.forward" }
-            publishDir = [
-                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 = [
-                enabled: false
-            ]
         }
 
         withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
             ext.prefix = { "${meta.id}.reverse" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/bigwig" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
         }
     }
 }
@@ -320,11 +158,6 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
                 ext.args2  = 'star_salmon'
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
             }
         }
     }
@@ -341,11 +174,6 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
                 ext.args2  = 'star_rsem'
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
             }
         }
     }
@@ -357,30 +185,12 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
 
 if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
     process {
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE' {
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT' {
             ext.prefix = { "${quant_type}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
         }
 
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_.*' {
             ext.args = '--assay_names counts,abundance'
-            publishDir = [
-                path: { "${params.outdir}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
-            ]
         }
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE' {
             ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
@@ -406,11 +216,6 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
                     params.deseq2_vst ? '--vst TRUE' : ''
                 ].join(' ').trim() }
                 ext.args2  = { params.pseudo_aligner }
-                publishDir = [
-                    path: { "${params.outdir}/${params.pseudo_aligner}/deseq2_qc" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*{RData,pca.vals.txt,plots.pdf,sample.dists.txt,size_factors,log}"
-                ]
             }
         }
     }