diff --git a/modules/local/bedtools_genomecov/nextflow.config b/modules/local/bedtools_genomecov/nextflow.config
index 85f3d34ae..6c61547d8 100644
--- a/modules/local/bedtools_genomecov/nextflow.config
+++ b/modules/local/bedtools_genomecov/nextflow.config
@@ -1,11 +1,4 @@
-
-if (!params.skip_alignment && !params.skip_bigwig) {
-    process {
-        withName: 'BEDTOOLS_GENOMECOV' {
-            ext.args   = '-split -du'
-            publishDir = [
-                enabled: false
-            ]
-        }
-    }
-}
+process.ext.args   = '-split -du'
+process.publishDir = [
+    enabled: false
+]
diff --git a/modules/local/dupradar/nextflow.config b/modules/local/dupradar/nextflow.config
index 3ade56ad5..96282836f 100644
--- a/modules/local/dupradar/nextflow.config
+++ b/modules/local/dupradar/nextflow.config
@@ -1,35 +1,27 @@
-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"
-                    ]
-                ]
-            }
-        }
-    }
-}
+process.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
index 68fecaa66..2bfc402d6 100644
--- a/modules/local/multiqc_custom_biotype/nextflow.config
+++ b/modules/local/multiqc_custom_biotype/nextflow.config
@@ -1,13 +1,5 @@
-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 }
-                ]
-            }
-        }
-    }
-}
+process.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..4a74e6f4b 100644
--- a/modules/nf-core/bbmap/bbsplit/nextflow.config
+++ b/modules/nf-core/bbmap/bbsplit/nextflow.config
@@ -1,20 +1,14 @@
-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
+process.ext.args   = 'build=1 ambiguous2=all maxindel=150000'
+process.publishDir = [
+    [
+        path: "${params.outdir}/bbsplit",
+        mode: params.publish_dir_mode,
+        pattern: '*.txt'
+    ],
+    [
+        path: "${params.outdir}/bbsplit",
+        mode: params.publish_dir_mode,
+        pattern: '*.fastq.gz',
+        saveAs: { params.save_bbsplit_reads ? it : null }
+    ]
+]
diff --git a/modules/nf-core/cat/fastq/nextflow.config b/modules/nf-core/cat/fastq/nextflow.config
index 64de2e49c..cfd3c7e84 100644
--- a/modules/nf-core/cat/fastq/nextflow.config
+++ b/modules/nf-core/cat/fastq/nextflow.config
@@ -1,9 +1,5 @@
-process {
-    withName: 'CAT_FASTQ' {
-        publishDir = [
-            path: { params.save_merged_fastq ? "${params.outdir}/fastq" : params.outdir },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> (filename.endsWith('.fastq.gz') && params.save_merged_fastq) ? filename : null }
-        ]
-    }
-}
+process.publishDir = [
+    path: "${params.outdir}/fastq",
+    mode: params.publish_dir_mode,
+    saveAs: { filename -> filename.equals('versions.yml') ? null : params.save_merged_fastq ? filename : null }
+]
diff --git a/modules/nf-core/preseq/lcextrap/nextflow.config b/modules/nf-core/preseq/lcextrap/nextflow.config
index e203e87e7..ac0dfc3db 100644
--- a/modules/nf-core/preseq/lcextrap/nextflow.config
+++ b/modules/nf-core/preseq/lcextrap/nextflow.config
@@ -1,21 +1,13 @@
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_preseq) {
-        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"
-                    ]
-                ]
-            }
-        }
-    }
-}
\ No newline at end of file
+process.ext.args   = '-verbose -bam -seed 1 -seg_len 100000000'
+process.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
index 9c05fb25a..c08deff96 100644
--- a/modules/nf-core/qualimap/rnaseq/nextflow.config
+++ b/modules/nf-core/qualimap/rnaseq/nextflow.config
@@ -1,13 +1,5 @@
-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 }
-                ]
-            }
-        }
-    }
-}
+process.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..7ca19c0ba 100644
--- a/modules/nf-core/sortmerna/nextflow.config
+++ b/modules/nf-core/sortmerna/nextflow.config
@@ -1,20 +1,14 @@
-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
+process.ext.args   = '--num_alignments 1 -v'
+process.publishDir = [
+    [
+        path: "${params.outdir}/sortmerna",
+        mode: params.publish_dir_mode,
+        pattern: "*.log"
+    ],
+    [
+        path: "${params.outdir}/sortmerna",
+        mode: params.publish_dir_mode,
+        pattern: "*.fastq.gz",
+        saveAs: { params.save_non_ribo_reads ? it : null }
+    ]
+]
diff --git a/modules/nf-core/stringtie/stringtie/nextflow.config b/modules/nf-core/stringtie/stringtie/nextflow.config
index dc0651458..6f5434179 100644
--- a/modules/nf-core/stringtie/stringtie/nextflow.config
+++ b/modules/nf-core/stringtie/stringtie/nextflow.config
@@ -1,17 +1,9 @@
-if (!params.skip_alignment) {
-    if (!params.skip_stringtie) {
-        process {
-            withName: 'STRINGTIE_STRINGTIE' {
-                ext.args   = { [
-                    '-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 }
-                ]
-            }
-        }
-    }
-}
\ No newline at end of file
+process.ext.args   = [
+    '-v',
+    params.stringtie_ignore_gtf ? '' : '-e'
+].join(' ').trim()
+process.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..cbc373cca 100644
--- a/modules/nf-core/subread/featurecounts/nextflow.config
+++ b/modules/nf-core/subread/featurecounts/nextflow.config
@@ -1,26 +1,11 @@
-if (!params.skip_alignment && !params.skip_qc) {
-    if (!params.skip_biotype_qc && params.featurecounts_group_type) {
-        process {
-            withName: 'SUBREAD_FEATURECOUNTS' {
-                ext.args   = { [
-                    '-B -C',
-                    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 }
-                ]
-            }
+process.ext.args   = [
+    '-B -C',
+    params.gencode ? "-g gene_type" : "-g $params.featurecounts_group_type",
+    "-t $params.featurecounts_feature_type"
+].join(' ').trim()
 
-            withName: 'MULTIQC_CUSTOM_BIOTYPE' {
-                publishDir = [
-                    path: { "${params.outdir}/${params.aligner}/featurecounts" },
-                    mode: params.publish_dir_mode,
-                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-                ]
-            }
-        }
-    }
-}
+process.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..5a7b63530 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -334,10 +334,6 @@ manifest {
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 
-// Workflow specific config
-includeConfig "./subworkflows/local/prepare_genome/nextflow.config"
-includeConfig './workflows/rnaseq/nextflow.config'
-
 // Function to ensure that resource requirements don't go beyond
 // a maximum limit
 def check_max(obj, type) {
diff --git a/subworkflows/local/prepare_genome/nextflow.config b/subworkflows/local/prepare_genome/nextflow.config
index 98a4b64fd..6bf95577e 100644
--- a/subworkflows/local/prepare_genome/nextflow.config
+++ b/subworkflows/local/prepare_genome/nextflow.config
@@ -1,7 +1,7 @@
 process {
     withName: 'GUNZIP_.*|MAKE_TRANSCRIPTS_FASTA' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -13,7 +13,7 @@ process {
 
     withName: 'UNTAR_.*|STAR_GENOMEGENERATE|STAR_GENOMEGENERATE_IGENOMES|HISAT2_BUILD' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome/index" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -22,7 +22,7 @@ process {
     withName: 'GFFREAD' {
         ext.args   = '--keep-exon-attrs -F -T'
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -30,7 +30,7 @@ process {
 
     withName: 'HISAT2_EXTRACTSPLICESITES' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome/index" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -42,7 +42,7 @@ process {
                 params.pseudo_aligner_kmer_size ? "-k ${params.pseudo_aligner_kmer_size}": ''
         ].join(' ').trim() }
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            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 }
         ]
@@ -51,7 +51,7 @@ process {
     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 },
+            path: params.save_reference ? "${params.outdir}/genome/index" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -60,7 +60,7 @@ process {
     withName: 'RSEM_PREPAREREFERENCE_GENOME' {
         ext.args   = '--star'
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
+            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 }
         ]
@@ -68,15 +68,15 @@ process {
 
     withName: 'GTF2BED' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${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' {
+    withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -85,7 +85,7 @@ process {
     withName: 'GTF_FILTER' {
         ext.args   = { params.skip_gtf_transcript_filter ?: '--skip_transcript_id_check' }
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
@@ -93,22 +93,18 @@ process {
 
     withName: 'CUSTOM_GETCHROMSIZES' {
         publishDir = [
-            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            path: params.save_reference ? "${params.outdir}/genome" : params.outdir,
             mode: params.publish_dir_mode,
             saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
         ]
     }
-}
 
-if (!params.skip_bbsplit && params.bbsplit_fasta_list) {
-    process {
-        withName: 'PREPARE_GENOME:BBMAP_BBSPLIT' {
-            ext.args   = 'build=1'
-            publishDir = [
-                path: { params.save_reference ? "${params.outdir}/genome/index" : params.outdir },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
-            ]
-        }
+    withName: 'BBMAP_BBSPLIT' {
+        ext.args   = 'build=1'
+        publishDir = [
+            path: params.save_reference ? "${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/nf-core/bam_markduplicates_picard/nextflow.config b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
index 2778db78d..149fc57c4 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
+++ b/subworkflows/nf-core/bam_markduplicates_picard/nextflow.config
@@ -1,41 +1,37 @@
-if (!params.skip_alignment) {
-    if (!params.skip_markduplicates && !params.with_umi) {
-        process {
-            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}/${params.aligner}" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.bam'
-                    ]
-                ]
-            }
+process {
+    withName: 'PICARD_MARKDUPLICATES' {
+        ext.args   = '--ASSUME_SORTED true --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
+        ext.prefix = { "${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}/${params.aligner}" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{bai,csi}'
-                ]
-            }
+    withName: 'SAMTOOLS_INDEX' {
+        ext.args   = { params.bam_csi_index ? '-c' : '' }
+        ext.prefix = { "${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}/${params.aligner}/samtools_stats" },
-                    mode: params.publish_dir_mode,
-                    pattern: '*.{stats,flagstat,idxstats}'
-                ]
-            }
-        }
+    withName: 'BAM_STATS_SAMTOOLS:.*' {
+        ext.prefix = { "${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/fastq_fastqc_umitools_fastp/nextflow.config b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
index 061689d5f..0e022833e 100644
--- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
+++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/nextflow.config
@@ -1,72 +1,58 @@
-if (!(params.skip_fastqc || params.skip_qc)) {
-    if (params.trimmer == 'fastp') {
-        process {
-            withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
-                ext.args   = '--quiet'
-            }
+process {
+    withName: 'FASTQC_RAW' {
+        ext.args   = '--quiet'
+    }
 
-            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 }
-                ]
-            }
-        }
+    withName: '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 }
+        ]
     }
-}
 
-if (!params.skip_trimming) {
-    if (params.trimmer == 'fastp') {
-        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 }
-                    ]
-                ]
-            }
-        }
+    withName: '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 }
+            ]
+        ]
     }
-}
 
-if (params.with_umi && !params.skip_umi_extract) {
-    process {
-        withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:UMITOOLS_EXTRACT' {
-            ext.args   = { [
-                    params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
-                    params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
-                    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 }
-                ]
+    withName: 'UMITOOLS_EXTRACT' {
+        ext.args   = { [
+                params.umitools_extract_method ? "--extract-method=${params.umitools_extract_method}" : '',
+                params.umitools_bc_pattern     ? "--bc-pattern='${params.umitools_bc_pattern}'" : '',
+                params.umitools_bc_pattern2    ? "--bc-pattern2='${params.umitools_bc_pattern2}'" : '',
+                params.umitools_umi_separator  ? "--umi-separator='${params.umitools_umi_separator}'" : ''
+        ].join(' ').trim() }
+        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..2cf1f3aae 100644
--- a/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
+++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config
@@ -1,5 +1,5 @@
 process {
-    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE' {
+    withName: 'FQ_SUBSAMPLE' {
         ext.args   = '--record-count 1000000 --seed 1'
         ext.prefix = { "${meta.id}.subsampled" }
         publishDir = [
@@ -7,7 +7,7 @@ process {
         ]
     }
 
-    withName: '.*:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT' {
+    withName: 'SALMON_QUANT' {
         ext.args   = '--skipQuant'
         publishDir = [
             enabled: false
diff --git a/workflows/rnaseq/nextflow.config b/workflows/rnaseq/nextflow.config
index f988d3d7c..80e46474b 100644
--- a/workflows/rnaseq/nextflow.config
+++ b/workflows/rnaseq/nextflow.config
@@ -1,176 +1,151 @@
-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"
-includeConfig "../../subworkflows/nf-core/fastq_subsample_fq_salmon/nextflow.config"
 
 //
 // 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 }
-            ]
-        }
+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: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:TXIMETA_TXIMPORT' {
-            ext.prefix = { "${quant_type}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
+    withName: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
+        ext.prefix = { "${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 = { "${params.pseudo_aligner}.merged.gene_counts" }
+    }
+    withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_SCALED' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
+    }
+    withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
+    }
+    withName: '.*:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
+    }
+
+    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,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+                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: '.*:QUANTIFY_STAR_SALMON:SE_.*' {
-            ext.prefix = { "${params.pseudo_aligner}.merged" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}" },
+    withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP' {
+        ext.args   = { [
+            meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
+            params.umitools_grouping_method ? "--method='${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.save_align_intermeds || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir,
                 mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.log') ? null : filename }
+                pattern: '*.bam',
+                saveAs: { params.save_align_intermeds || params.save_umi_intermeds ? it : null }
             ]
-        }
-        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts" }
-        }
-        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_SCALED' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
-        }
-        withName: '.*:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
-        }
-        withName: '.*:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
-        }
-    }
-
-    if (params.with_umi) {
-        process {
-            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' {
-                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}/${params.aligner}/umitools" },
-                        mode: params.publish_dir_mode,
-                        pattern: '*.tsv'
-                    ],
-                    [
-                        path: { params.save_align_intermeds || params.save_umi_intermeds ? "${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}'
-                ]
-            }
-        }
+        ]
+    }
+
+    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}'
+        ]
     }
 }
 
@@ -178,90 +153,84 @@ if (!params.skip_alignment && params.aligner == 'star_salmon') {
 // 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: { ( ['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 },
+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 }
+        ]
+    }
+
+    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}/${params.aligner}/umitools",
                 mode: params.publish_dir_mode,
-                pattern: "*.bam",
-                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
-            ]
-        }
-
-        withName: 'NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
-            ext.args   = { params.bam_csi_index ? '-c' : '' }
-            publishDir = [
-                path: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? "${params.outdir}/${params.aligner}" : params.outdir },
+                pattern: '*.tsv'
+            ],
+            [
+                path: params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? "${params.outdir}/${params.aligner}" : params.outdir,
                 mode: params.publish_dir_mode,
-                pattern: "*.{bai,csi}",
-                saveAs: { ( ['star_salmon','hisat2'].contains(params.aligner) &&
-                        ( params.save_align_intermeds || ( !params.with_umi && params.skip_markduplicates ) )
-                    ) || params.save_align_intermeds || params.skip_markduplicates ? it : null }
+                pattern: '*.bam',
+                saveAs: { params.save_align_intermeds || params.with_umi || params.save_umi_intermeds ? it : null }
             ]
-        }
-    }
-
-    if (params.with_umi && ['star_salmon','hisat2'].contains(params.aligner)) {
-        process {
-            withName: '.*:BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME:UMITOOLS_DEDUP' {
-                ext.args   = { [
-                    meta.single_end                 ? '' : '--unpaired-reads=discard --chimeric-pairs=discard',
-                    params.umitools_grouping_method ? "--method='${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.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}'
-                ]
-            }
-        }
+        ]
+    }
+
+    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}'
+        ]
     }
 }
 
@@ -269,39 +238,37 @@ if (!params.skip_alignment) {
 // bigWig coverage options
 //
 
-if (!params.skip_alignment && !params.skip_bigwig) {
-    process {
-        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
-            ext.prefix = { "${meta.id}.clip.forward" }
-            publishDir = [
-                enabled: false
-            ]
-        }
+process {
+    withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
+        ext.prefix = { "${meta.id}.clip.forward" }
+        publishDir = [
+            enabled: false
+        ]
+    }
 
-        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
-            ext.prefix = { "${meta.id}.forward" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/bigwig" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
+        ext.prefix = { "${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 = { "${meta.id}.clip.reverse" }
-            publishDir = [
-                enabled: false
-            ]
-        }
+    withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
+        ext.prefix = { "${meta.id}.clip.reverse" }
+        publishDir = [
+            enabled: false
+        ]
+    }
 
-        withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
-            ext.prefix = { "${meta.id}.reverse" }
-            publishDir = [
-                path: { "${params.outdir}/${params.aligner}/bigwig" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
+        ext.prefix = { "${meta.id}.reverse" }
+        publishDir = [
+            path: "${params.outdir}/${params.aligner}/bigwig",
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }
 
@@ -309,45 +276,35 @@ if (!params.skip_alignment && !params.skip_bigwig) {
 // DESeq2 QC options
 //
 
-if (!params.skip_alignment && params.aligner == 'star_salmon') {
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_STAR_SALMON' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    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}"
-                ]
-            }
-        }
+process {
+    withName: 'DESEQ2_QC_STAR_SALMON' {
+        ext.args   = { [
+            "--id_col 1",
+            "--sample_suffix ''",
+            "--count_col 3",
+            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}"
+        ]
     }
-}
 
-if (!params.skip_alignment && params.aligner == 'star_rsem') {
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_RSEM' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    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}"
-                ]
-            }
-        }
+    withName: 'DESEQ2_QC_RSEM' {
+        ext.args   = { [
+            "--id_col 1",
+            "--sample_suffix ''",
+            "--count_col 3",
+            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}"
+        ]
     }
 }
 
@@ -355,63 +312,56 @@ if (!params.skip_alignment && params.aligner == 'star_rsem') {
 // Pseudo-alignment options
 //
 
-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 }
-            ]
-        }
+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}/${params.pseudo_aligner}" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT' {
+        ext.prefix = { "${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 = { "${params.pseudo_aligner}.merged.gene_counts" }
-        }
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
-        }
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
-        }
-        withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT' {
-            ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
-        }
-    }
-
-    if (!params.skip_qc & !params.skip_deseq2_qc) {
-        process {
-            withName: 'DESEQ2_QC_PSEUDO' {
-                ext.args   = { [
-                    "--id_col 1",
-                    "--sample_suffix ''",
-                    "--count_col 3",
-                    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}"
-                ]
-            }
-        }
+    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 = { "${params.pseudo_aligner}.merged.gene_counts" }
+    }
+    withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_scaled" }
+    }
+    withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.gene_counts_length_scaled" }
+    }
+    withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT' {
+        ext.prefix = { "${params.pseudo_aligner}.merged.transcript_counts" }
+    }
+    withName: 'DESEQ2_QC_PSEUDO' {
+        ext.args   = { [
+            "--id_col 1",
+            "--sample_suffix ''",
+            "--count_col 3",
+            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}"
+        ]
     }
 }