diff --git a/src/Snakefile b/src/Snakefile
index 8565c10794f3be0d0c5d81c9851d097159c47537..d10e7d1ab93db4b29461c9bd7e1cefb711899797 100755
--- a/src/Snakefile
+++ b/src/Snakefile
@@ -835,7 +835,7 @@ if pairedEnd:
         conda: "condaEnvironments/fastqc.yaml"
         # benchmark: LOG_BENCHMARK_dir + "/fastqc_BT.{sample}.benchmark"
         singularity: singularity_conda
-        group: "samplePreprocessing"
+        # group: "samplePreprocessing"
         params:
             outdir = FASTQC_BT_dir
         shell:
@@ -860,7 +860,7 @@ else:
         conda: "condaEnvironments/fastqc.yaml"
         # benchmark: LOG_BENCHMARK_dir + "/fastqc_BT.{sample}.benchmark"
         singularity: singularity_conda
-        group: "samplePreprocessing"
+        # group: "samplePreprocessing"
         params:
             outdir = FASTQC_BT_dir
         shell:
@@ -893,7 +893,7 @@ if pairedEnd:
         conda: "condaEnvironments/trimmomatic.yaml"
         # benchmark: LOG_BENCHMARK_dir + "/trimming_PE.{sample}.benchmark"
         singularity: singularity_conda
-        group: "samplePreprocessing"
+        # group: "samplePreprocessing"
         params:
             ILLUMINACLIP = config["trimming"]["trimmomatic_ILLUMINACLIP"],
             trailing     = config["trimming"]["trimmomatic_trailing"],
@@ -923,7 +923,7 @@ else:
         threads: threadsMax
         conda: "condaEnvironments/trimmomatic.yaml"
         singularity: singularity_conda
-        group: "samplePreprocessing"
+        # group: "samplePreprocessing"
         params:
             ILLUMINACLIP = config["trimming"]["trimmomatic_ILLUMINACLIP"],
             trailing     = config["trimming"]["trimmomatic_trailing"],
@@ -1051,7 +1051,7 @@ rule samtools_SAM_TO_BAM:
     conda: "condaEnvironments/picard_samtools.yaml"
     # benchmark: LOG_BENCHMARK_dir + "/samtools_SAM_TO_BAM.{sample}.benchmark"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     shell:
         """
             samtools sort -o {output.sortedBam:q} --threads {threads} {input.bam:q} &&
@@ -1079,7 +1079,7 @@ rule Picard_cleanSAM:
     conda: "condaEnvironments/picard_samtools.yaml"
     # benchmark: LOG_BENCHMARK_dir + "/Picard_cleanSAM.{sample}.benchmark"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     shell:
         """
             {picard_command} CleanSam \
@@ -1109,7 +1109,7 @@ if pairedEnd:
         conda: "condaEnvironments/picard_samtools.yaml"
         # benchmark: LOG_BENCHMARK_dir + "/Picard_FixMateInformation.{sample}.benchmark"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         shell:
             """
                 {picard_command} FixMateInformation \
@@ -1138,7 +1138,7 @@ rule Picard_AddOrReplaceReadGroups:
     conda: "condaEnvironments/picard_samtools.yaml"
     # benchmark: LOG_BENCHMARK_dir + "/Picard_AddOrReplaceReadGroups.{sample}.benchmark"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
         RGID = lambda wildcards: RGFields[wildcards.sample]["ID"], # Read Group ID
         RGLB = lambda wildcards: RGFields[wildcards.sample]["LB"], # Read Group library
@@ -1179,7 +1179,7 @@ rule Picard_ReorderSam:
     conda: "condaEnvironments/picard_samtools.yaml"
     # benchmark: LOG_BENCHMARK_dir + "/Picard_ReorderSam.{sample}.benchmark"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
     shell:
         """
@@ -1204,7 +1204,7 @@ if config["output"]["doBaseRecalibration"]:
         threads: threadsMax
         conda: "condaEnvironments/gatk.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         params:
             knownSNPs        = file_knownSNPs,
             knownIndels      = file_knownINDELS,
@@ -1237,7 +1237,7 @@ if config["output"]["doBaseRecalibration"]:
         threads: threadsMax
         conda: "condaEnvironments/gatk.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         # benchmark: LOG_BENCHMARK_dir + "/GATK_printReadsBQSR.{sample}.benchmark"
         params:
             fasta = config["additionalInput"]["refGenome_fasta"]
@@ -1264,7 +1264,7 @@ if config["output"]["doBaseRecalibration"]:
         threads: threadsMax
         conda: "condaEnvironments/gatk.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         # benchmark: LOG_BENCHMARK_dir + "/GATK_baseRecalibration2.{sample}.benchmark"
         params:
             knownSNPs        = file_knownSNPs,
@@ -1301,7 +1301,7 @@ if config["output"]["doBaseRecalibration"]:
         threads: 1
         conda: "condaEnvironments/gatk.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         # benchmark: LOG_BENCHMARK_dir + "/GATK_analyzeCovariates.{sample}.benchmark"
         params:
             fasta = config["additionalInput"]["refGenome_fasta"]
@@ -1353,7 +1353,7 @@ rule postalign_remove_chrMAndUnassembledChr:
     # benchmark: LOG_BENCHMARK_dir + "/postalign_remove_chrMAndUnassembledChr.{sample}.benchmark"
     conda: "condaEnvironments/picard_samtools.yaml"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
     shell:
         """ samtools index {input.bam:q} &&
@@ -1381,7 +1381,7 @@ rule markDuplicates_Picardtools:
     # benchmark: LOG_BENCHMARK_dir + "/markDuplicates_Picardtools.{sample}.benchmark"
     conda: "condaEnvironments/picard_samtools.yaml"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
         ValidationStringency = config["postalign"]["ValidationStringencyMarkDuplicates"],
         removeDuplicates     = "false",
@@ -1411,7 +1411,7 @@ rule computeLibraryComplexity:
     conda: "condaEnvironments/bedtools.yaml"
     singularity: singularity_conda
     params:
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     shell:
     # Taken from https://github.com/kundajelab/atac_dnase_pipelines/blob/72ed6ba2502cca074c51740b612cbc6ebea07b08/modules/postalign_bam.bds
     # Implementing the ENCODE ATAC-Seq library complexity guidelines
@@ -1440,7 +1440,7 @@ rule removeDuplicates:
     # benchmark: LOG_BENCHMARK_dir + "/removeDuplicates.{sample}.benchmark"
     conda: "condaEnvironments/picard_samtools.yaml"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
         removeReadsWithFlags = 1804, # read or mate unmapped, not primary alignment, read fails platform/vendor quality checks, read is PCR or optical duplicate
         keepReadsWithFlags   = "-f" + str(duplicates_keepReadsFlag) if pairedEnd else ""# dependent on single-end vs paired-end
@@ -1470,7 +1470,7 @@ rule postalign_MAPQ:
     # benchmark: LOG_BENCHMARK_dir + "/postalign_MAPQ.{sample}.benchmark"
     conda: "condaEnvironments/picard_samtools.yaml"
     singularity: singularity_conda
-    group: "sampleProcessing"
+    # group: "sampleProcessing"
     params:
         minMAPQ = minMAPQscore
     shell:
@@ -1508,7 +1508,7 @@ if doRSSAdjustment:
         # benchmark: LOG_BENCHMARK_dir + "/postaling_RSS.{sample}.benchmark"
         conda: "condaEnvironments/picard_samtools.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         params:
             adjustRSS_forward = config["postalign"]["adjustRSS_forward"],
             adjustRSS_reverse = -config["postalign"]["adjustRSS_reverse"]
@@ -1566,7 +1566,7 @@ if doRSSAdjustment:
          # benchmark: LOG_BENCHMARK_dir + "/Picard_sortFinal.{sample}.benchmark"
          conda: "condaEnvironments/picard_samtools.yaml"
          singularity: singularity_conda
-         group: "sampleProcessing"
+         # group: "sampleProcessing"
          params:
          shell:
             """
@@ -1594,7 +1594,7 @@ if doRSSAdjustment:
          # benchmark: LOG_BENCHMARK_dir + "/Picard_cleanSamFinal.{sample}.benchmark"
          conda: "condaEnvironments/picard_samtools.yaml"
          singularity: singularity_conda
-         group: "sampleProcessing"
+         # group: "sampleProcessing"
          params:
          shell:
             """
@@ -1620,7 +1620,7 @@ if doRSSAdjustment:
         # benchmark: LOG_BENCHMARK_dir + "/Picard_FixMateInformationFinal.{sample}.benchmark"
         conda: "condaEnvironments/picard_samtools.yaml"
         singularity: singularity_conda
-        group: "sampleProcessing"
+        # group: "sampleProcessing"
         shell:
             """
                 {picard_command} FixMateInformation \
@@ -1820,7 +1820,7 @@ rule macs2_stringent:
         pairedEndString = macs2_pairedEndMode,
         keepDuplicates  = "--keep-dup all",
         controlFile = lambda wildcards: getControlSample(wildcards.basename)
-    group: "peaks"
+    # group: "peaks"
     shell:
         """PYTHONPATH="" &&
         macs2 callpeak \
@@ -1951,7 +1951,7 @@ rule filterPeaks:
     log:
     message: "{ruleDisplayMessage}Exclude blacklist regions for file {input.bed}..."
     threads: 1
-    group: "peaks"
+    # group: "peaks"
     params:
         blacklistRegions = config["additionalInput"]["blacklistRegions"]
     conda: "condaEnvironments/bedtools.yaml"
@@ -2274,7 +2274,7 @@ rule deeptools_plotEnrichment_frip_individual:
         plotTitle = "FRiP score",
         heightPDF = 15, # can be fixed, as long as sample names are not too long. Default is 10
         widthPDF  = max(10, nSamplesUnique * 1 * 0.4) # has to be flexible due to no. of samples on X
-    group: "peaks"
+    # group: "peaks"
     shell:
         """
             plotEnrichment \