diff --git a/conf/modules.config b/conf/modules.config
index dadf360d..79a679af 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -101,7 +101,6 @@ process {
 // Read QC and trimming options
 //
 
-if (!(params.skip_fastqc || params.skip_qc)) {
     process {
         withName: 'FASTQC' {
             ext.args = '--quiet'
@@ -119,9 +118,7 @@ if (!(params.skip_fastqc || params.skip_qc)) {
             ]
         }
     }
-}
 
-if (!params.skip_trimming) {
     process {
         withName: 'TRIMGALORE' {
             ext.args   = {
@@ -159,7 +156,6 @@ if (!params.skip_trimming) {
             ]
         }
     }
-}
 
 process {
     withName: 'NFCORE_CHIPSEQ:CHIPSEQ:.*:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
@@ -192,7 +188,6 @@ process {
     }
 }
 
-if (params.aligner == 'bwa') {
     process {
         withName: 'BWA_MEM' {
             ext.args   = {
@@ -212,9 +207,7 @@ if (params.aligner == 'bwa') {
             ]
         }
     }
-}
 
-if (params.aligner == 'bowtie2') {
     process {
         withName: 'BOWTIE2_ALIGN' {
             ext.args   = {
@@ -240,9 +233,7 @@ if (params.aligner == 'bowtie2') {
             ]
         }
     }
-}
 
-if (params.aligner == 'chromap') {
     process {
         withName: 'CHROMAP_INDEX' {
             publishDir = [
@@ -264,9 +255,7 @@ if (params.aligner == 'chromap') {
             ]
         }
     }
-}
 
-if (params.aligner == 'star') {
     process {
         withName: '.*:ALIGN_STAR:STAR_ALIGN' {
             ext.args   = [
@@ -300,7 +289,6 @@ if (params.aligner == 'star') {
             ]
         }
     }
-}
 
 process {
     withName: 'PICARD_MERGESAMFILES' {
@@ -480,7 +468,6 @@ process {
     }
 }
 
-if (!params.skip_picard_metrics) {
     process {
         withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
             ext.args   = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp'
@@ -499,9 +486,7 @@ if (!params.skip_picard_metrics) {
             ]
         }
     }
-}
 
-if (!params.skip_preseq) {
     process {
         withName: 'PRESEQ_LCEXTRAP' {
             ext.args   = '-verbose -bam -seed 1'
@@ -513,9 +498,7 @@ if (!params.skip_preseq) {
             ]
         }
     }
-}
 
-if (!params.skip_plot_profile) {
     process {
         withName: 'DEEPTOOLS_COMPUTEMATRIX' {
             ext.args   = 'scale-regions --regionBodyLength 1000 --beforeRegionStartLength 3000 --afterRegionStartLength 3000 --missingDataAsZero --skipZeros --smartLabels'
@@ -545,9 +528,7 @@ if (!params.skip_plot_profile) {
             ]
         }
     }
-}
 
-if (!params.skip_plot_fingerprint) {
     process {
         withName: 'DEEPTOOLS_PLOTFINGERPRINT' {
             ext.args   = { [
@@ -563,7 +544,6 @@ if (!params.skip_plot_fingerprint) {
             ]
         }
     }
-}
 
 process {
     withName: 'MACS3_CALLPEAK' {
@@ -599,7 +579,6 @@ process {
     }
 }
 
-if (!params.skip_peak_annotation) {
     process {
         withName: '.*:BAM_PEAKS_CALL_QC_ANNOTATE_MACS3_HOMER:HOMER_ANNOTATEPEAKS' {
             ext.args   = '-gid'
@@ -612,7 +591,6 @@ if (!params.skip_peak_annotation) {
         }
     }
 
-    if (!params.skip_peak_qc) {
         process {
             withName: 'PLOT_MACS3_QC' {
                 ext.args   = '-o ./ -p macs3_peak'
@@ -633,10 +611,7 @@ if (!params.skip_peak_annotation) {
                 ]
             }
         }
-    }
-}
 
-if (!params.skip_consensus_peaks) {
     process {
         withName: 'MACS3_CONSENSUS' {
             ext.when   = { meta.multiple_groups || meta.replicates_exist }
@@ -659,7 +634,6 @@ if (!params.skip_consensus_peaks) {
         }
     }
 
-    if (!params.skip_peak_annotation) {
         process {
             withName: '.*:BED_CONSENSUS_QUANTIFY_QC_BEDTOOLS_FEATURECOUNTS_DESEQ2:HOMER_ANNOTATEPEAKS' {
                 ext.args   = '-gid'
@@ -680,9 +654,7 @@ if (!params.skip_consensus_peaks) {
                 ]
             }
         }
-    }
 
-    if (!params.skip_deseq2_qc) {
         process {
             withName: 'DESEQ2_QC' {
                 ext.when   = { meta.multiple_groups && meta.replicates_exist }
@@ -700,10 +672,7 @@ if (!params.skip_consensus_peaks) {
                 ]
             }
         }
-    }
-}
 
-if (!params.skip_igv) {
     process {
         withName: 'IGV' {
             publishDir = [
@@ -720,9 +689,7 @@ if (!params.skip_igv) {
             ]
         }
     }
-}
 
-if (!params.skip_multiqc) {
     process {
         withName: 'MULTIQC' {
             ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
@@ -733,4 +700,3 @@ if (!params.skip_multiqc) {
             ]
         }
     }
-}
diff --git a/workflows/chipseq.nf b/workflows/chipseq.nf
index ba615ab7..567ab9b9 100644
--- a/workflows/chipseq.nf
+++ b/workflows/chipseq.nf
@@ -61,30 +61,6 @@ include { BAM_MARKDUPLICATES_PICARD        } from '../subworkflows/nf-core/bam_m
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// JSON files required by BAMTools for alignment filtering
-ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
-ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
-
-// Header files for MultiQC
-ch_spp_nsc_header           = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
-ch_spp_rsc_header           = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
-ch_spp_correlation_header   = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
-ch_peak_count_header        = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
-ch_frip_score_header        = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
-ch_peak_annotation_header   = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
-ch_deseq2_pca_header        = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
-ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))
-
-// Save AWS IGenomes file containing annotation version
-def anno_readme = params.genomes[ params.genome ]?.readme
-if (anno_readme && file(anno_readme).exists()) {
-    file("${params.outdir}/genome/").mkdirs()
-    file(anno_readme).copyTo("${params.outdir}/genome/")
-}
-
-
-// // Info required for completion email and summary
-// def multiqc_report = []
 
 workflow CHIPSEQ {
 
@@ -103,6 +79,28 @@ workflow CHIPSEQ {
     ch_star_index    // channel: path(star/index/)
 
     main:
+
+    // JSON files required by BAMTools for alignment filtering
+    ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
+    ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
+
+    // Header files for MultiQC
+    ch_spp_nsc_header           = file("$projectDir/assets/multiqc/spp_nsc_header.txt", checkIfExists: true)
+    ch_spp_rsc_header           = file("$projectDir/assets/multiqc/spp_rsc_header.txt", checkIfExists: true)
+    ch_spp_correlation_header   = file("$projectDir/assets/multiqc/spp_correlation_header.txt", checkIfExists: true)
+    ch_peak_count_header        = file("$projectDir/assets/multiqc/peak_count_header.txt", checkIfExists: true)
+    ch_frip_score_header        = file("$projectDir/assets/multiqc/frip_score_header.txt", checkIfExists: true)
+    ch_peak_annotation_header   = file("$projectDir/assets/multiqc/peak_annotation_header.txt", checkIfExists: true)
+    ch_deseq2_pca_header        = Channel.value(file("$projectDir/assets/multiqc/deseq2_pca_header.txt", checkIfExists: true))
+    ch_deseq2_clustering_header = Channel.value(file("$projectDir/assets/multiqc/deseq2_clustering_header.txt", checkIfExists: true))
+
+    // Save AWS IGenomes file containing annotation version
+    def anno_readme = params.genomes[ params.genome ]?.readme
+    if (anno_readme && file(anno_readme).exists()) {
+        file("${params.outdir}/genome/").mkdirs()
+        file(anno_readme).copyTo("${params.outdir}/genome/")
+    }
+
     ch_multiqc_files = channel.empty()
 
     //