diff --git a/tests/pipeline/test.nf.test.snap b/tests/pipeline/test.nf.test.snap
index 8bc0edbf..32582165 100644
--- a/tests/pipeline/test.nf.test.snap
+++ b/tests/pipeline/test.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T03:10:19+0000"
     },
diff --git a/tests/pipeline/test_aligner_bowtie2.nf.test.snap b/tests/pipeline/test_aligner_bowtie2.nf.test.snap
index 033fcd05..2e417fca 100644
--- a/tests/pipeline/test_aligner_bowtie2.nf.test.snap
+++ b/tests/pipeline/test_aligner_bowtie2.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BOWTIE2_ALIGN={bowtie2=2.4.4, pigz=2.6, samtools=1.16.1}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BOWTIE2_ALIGN={bowtie2=2.4.4, pigz=2.6, samtools=1.17}, BOWTIE2_BUILD={bowtie2=2.4.4}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T16:33:44+0000"
     },
diff --git a/tests/pipeline/test_aligner_chromap.nf.test.snap b/tests/pipeline/test_aligner_chromap.nf.test.snap
index 3bf9d3ae..36ca994a 100644
--- a/tests/pipeline/test_aligner_chromap.nf.test.snap
+++ b/tests/pipeline/test_aligner_chromap.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.16.1}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CHROMAP_CHROMAP={chromap=0.2.4-r467, samtools=1.17}, CHROMAP_INDEX={chromap=0.2.4-r467}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T14:32:52+0000"
     },
diff --git a/tests/pipeline/test_aligner_star.nf.test.snap b/tests/pipeline/test_aligner_star.nf.test.snap
index c3efc510..964dbaab 100644
--- a/tests/pipeline/test_aligner_star.nf.test.snap
+++ b/tests/pipeline/test_aligner_star.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, STAR_ALIGN={star=2.6.1d}, STAR_GENOMEGENERATE={star=2.6.1d}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, STAR_ALIGN={star=2.6.1d}, STAR_GENOMEGENERATE={star=2.6.1d}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T14:22:15+0000"
     },
diff --git a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap
index f9b22758..9e90f1e1 100644
--- a/tests/pipeline/test_skip_consensus_peaks.nf.test.snap
+++ b/tests/pipeline/test_skip_consensus_peaks.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, TRIMGALORE={cutadapt=3.4, trimgalore=0.6.7}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T14:47:53+0000"
     },
diff --git a/tests/pipeline/test_skip_trimming.nf.test.snap b/tests/pipeline/test_skip_trimming.nf.test.snap
index 8a17514f..9c04b88a 100644
--- a/tests/pipeline/test_skip_trimming.nf.test.snap
+++ b/tests/pipeline/test_skip_trimming.nf.test.snap
@@ -10,7 +10,7 @@
     },
     "software_versions": {
         "content": [
-            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.16.1}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.16.1}, SAMTOOLS_IDXSTATS={samtools=1.16.1}, SAMTOOLS_INDEX={samtools=1.16.1}, SAMTOOLS_SORT={samtools=1.16.1}, SAMTOOLS_STATS={samtools=1.16.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
+            "{ANNOTATE_BOOLEAN_PEAKS={sed=4.7}, BAMTOOLS_FILTER={bamtools=2.5.2, samtools=1.15.1}, BAM_REMOVE_ORPHANS={samtools=1.15.1}, BEDTOOLS_GENOMECOV={bedtools=2.30.0}, BWA_INDEX={bwa=0.7.17-r1188}, BWA_MEM={bwa=0.7.17-r1188, samtools=1.17}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, CUSTOM_GETCHROMSIZES={getchromsizes=1.16.1}, DEEPTOOLS_COMPUTEMATRIX={deeptools=3.5.1}, DEEPTOOLS_PLOTFINGERPRINT={deeptools=3.5.1}, DEEPTOOLS_PLOTHEATMAP={deeptools=3.5.1}, DEEPTOOLS_PLOTPROFILE={deeptools=3.5.1}, FASTQC={fastqc=0.11.9}, FRIP_SCORE={bedtools=2.30.0, samtools=1.15.1}, GENOME_BLACKLIST_REGIONS={bedtools=2.30.0}, GTF2BED={perl=5.26.2}, HOMER_ANNOTATEPEAKS_CONSENSUS={homer=4.11}, HOMER_ANNOTATEPEAKS_MACS2={homer=4.11}, IGV={python=3.8.3}, MACS2_CALLPEAK={macs2=2.2.7.1}, MACS2_CONSENSUS={python=3.10.0, r-base=4.1.1}, PHANTOMPEAKQUALTOOLS={phantompeakqualtools=1.2.2}, PICARD_COLLECTMULTIPLEMETRICS={picard=3.0.0}, PICARD_MARKDUPLICATES={picard=3.0.0}, PICARD_MERGESAMFILES={picard=3.0.0}, PLOT_HOMER_ANNOTATEPEAKS={r-base=4.0.3}, PLOT_MACS2_QC={r-base=4.0.3}, SAMPLESHEET_CHECK={python=3.8.3}, SAMTOOLS_FLAGSTAT={samtools=1.17}, SAMTOOLS_IDXSTATS={samtools=1.17}, SAMTOOLS_INDEX={samtools=1.17}, SAMTOOLS_SORT={samtools=1.17}, SAMTOOLS_STATS={samtools=1.17}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, UCSC_BEDGRAPHTOBIGWIG={ucsc=377}, Workflow={nf-core/chipseq=2.1.0dev}}"
         ],
         "timestamp": "2023-06-23T17:20:02+0000"
     },