diff --git a/tests/test_contamination_tech_reps.nf.test.snap b/tests/test_contamination_tech_reps.nf.test.snap
index 9441f4c5..47b6891d 100644
--- a/tests/test_contamination_tech_reps.nf.test.snap
+++ b/tests/test_contamination_tech_reps.nf.test.snap
@@ -34,13 +34,13 @@
     },
     "software_versions": {
         "content": [
-            "{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE2_ALIGN_CDNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_NCRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE2_ALIGN_TRNA={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CAT_FASTQ={cat=8.3}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FILTER_STATS={BusyBox=1.32.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, GAWK_CDNA={gawk=5.3.0}, GAWK_NCRNA={gawk=5.3.0}, INDEX_CDNA={bowtie2=2.5.2}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, INDEX_NCRNA={bowtie2=2.5.2}, INDEX_TRNA={bowtie2=2.5.2}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, STATS_GAWK_CDNA={gawk=5.3.0}, STATS_GAWK_NCRNA={gawk=5.3.0}, STATS_GAWK_TRNA={gawk=5.3.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-02T13:29:37.770610046"
+        "timestamp": "2024-10-08T23:16:26.853242481"
     },
     "mirna_quant_bam": {
         "content": [
diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap
index db381a2e..7724ffbd 100644
--- a/tests/test_mirgenedb.nf.test.snap
+++ b/tests/test_mirgenedb.nf.test.snap
@@ -1,10 +1,10 @@
 {
     "genome_quant_bam": {
         "content": [
-            "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,201486e8c88b0dbb639776f9dacefe66",
+            "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,6b1d2b924593096358494dda37b46770",
             "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,aa37c5da7c2b4505ce58c3a21f97121c",
-            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,5679af445f4628e0f4137f339319c950",
-            "Control_N1_mature_hairpin_genome.sorted.stats:md5,4da4f877f06083f616a0d76edd04ea22",
+            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,3c5f51cd7136eed5e97847ad7b857d23",
+            "Control_N1_mature_hairpin_genome.sorted.stats:md5,a7f2dd17a34c8f0b669a774404247394",
             "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,5bb521c495f1c450835299b1eb88dc84",
             "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,6a8ad3be2ca0fa924fd32a04293d4ce4",
             "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,d92f9eae7657418858e6d2b69436f74f",
@@ -15,17 +15,17 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-20T13:36:32.067039888"
+        "timestamp": "2024-10-08T23:23:13.57712901"
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_FQ2FA={seqkit=2.8.0}, SEQKIT_REPLACE={seqkit=2.8.0}, Workflow={nf-core/smrnaseq=v2.4.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T20:13:41.274631809"
+        "timestamp": "2024-10-08T23:23:13.407922799"
     },
     "mirna_quant_bam": {
         "content": [
@@ -34,25 +34,25 @@
             "Clone9_N1_mature.sorted.flagstat:md5,adf40ba27907b6ef726d6c5923a731b9",
             "Clone9_N1_mature.sorted.idxstats:md5,8302f401476f5c8fee3333e1c742c05e",
             "Control_N1_mature.sorted.flagstat:md5,f8df7690d20014518f47dc2fe39debec",
-            "Control_N1_mature.sorted.stats:md5,35a03b446785dbf240d755ea9edac0f6",
-            "Clone9_N1_mature.sorted.stats:md5,d2cb555133269b4503e4eb490dd81b3e",
+            "Control_N1_mature.sorted.stats:md5,3c952d69ed81186976ede053c847e109",
+            "Clone9_N1_mature.sorted.stats:md5,873e4f40e377cc445ace1ac48354729d",
             "Control_N1_mature.sorted.idxstats:md5,b7a382b1d0f5cba6cb94b3b5a6b18f84",
             true,
             "Control_N1_mature_hairpin.sorted.idxstats:md5,79dc5e82ff88e7379c893549224cd87f",
             "Control_N1_mature_hairpin.sorted.flagstat:md5,1dc7b98f0014a99a20de7c09a6b95340",
             "Clone9_N1_mature_hairpin.sorted.idxstats:md5,f3ed5bf23f73d41c42d3da0bf30f89ea",
-            "Clone9_N1_mature_hairpin.sorted.stats:md5,9fda01757030fe96a60171965117b2e4",
+            "Clone9_N1_mature_hairpin.sorted.stats:md5,c306ef4c5b1e23a3d032b532cf916fc1",
             true,
             true,
             true,
-            "Control_N1_mature_hairpin.sorted.stats:md5,a96b6d37b444f52c66a3dac9d7de0f36",
+            "Control_N1_mature_hairpin.sorted.stats:md5,3e82fa30bfafcab2e8fb2f247e591959",
             "Clone9_N1_mature_hairpin.sorted.flagstat:md5,678f4f9e98c3e1fcc5af54e8dd06fbbc"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T15:14:06.231457002"
+        "timestamp": "2024-10-08T23:23:13.503940378"
     },
     "mirdeep2": {
         "content": [
diff --git a/tests/test_nextflex.nf.test.snap b/tests/test_nextflex.nf.test.snap
index 6cbb32d8..84604361 100644
--- a/tests/test_nextflex.nf.test.snap
+++ b/tests/test_nextflex.nf.test.snap
@@ -34,32 +34,32 @@
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-02T13:42:51.224838419"
+        "timestamp": "2024-10-08T23:25:57.880948228"
     },
     "mirna_quant_bam": {
         "content": [
             "sample2_mature.sorted.idxstats:md5,9688f02beeebf9a590dc81e49415ede9",
             "sample1_mature.sorted.flagstat:md5,7d61ae305e545c7a66ef8d23a0c8be25",
-            "sample2_mature.sorted.stats:md5,6b4ae70a722d0c83e86691114de5e592",
-            "sample3_mature.sorted.stats:md5,f7c7bfcf9538cc377fcdc6a268b5ee74",
+            "sample2_mature.sorted.stats:md5,1a2146975784f51e98f4208f4562a4e6",
+            "sample3_mature.sorted.stats:md5,d1c48aac54b7b741e1108d97e9231232",
             "sample3_mature.sorted.flagstat:md5,1aae00444143bce06cb0f8cf31deb8e4",
             "sample3_mature.sorted.idxstats:md5,9688f02beeebf9a590dc81e49415ede9",
-            "sample1_mature.sorted.stats:md5,8654e47669c01b0faaab664ba2770a17",
+            "sample1_mature.sorted.stats:md5,80f9a8fe5d498265223e95d9dd04a89a",
             "sample2_mature.sorted.flagstat:md5,1aae00444143bce06cb0f8cf31deb8e4",
             "sample1_mature.sorted.idxstats:md5,6db0cfab41307285fe5c89dfe95b5d46",
-            "sample3_mature_hairpin.sorted.stats:md5,122c9151ad16c284b3837f53328fce75",
+            "sample3_mature_hairpin.sorted.stats:md5,e725f70ac1e4e4007714b19e588cbc46",
             "sample2_mature_hairpin.sorted.flagstat:md5,4e201dd868164d0c53142888dd6ca238",
             "sample1_mature_hairpin.sorted.flagstat:md5,7ed3ab444077ddf6c334845e9c4ce75e",
             "sample1_mature_hairpin.sorted.idxstats:md5,7b7d142caee6cccbb6d83c8e6568a951",
             "sample3_mature_hairpin.sorted.flagstat:md5,4e201dd868164d0c53142888dd6ca238",
-            "sample2_mature_hairpin.sorted.stats:md5,387aeaf6401470f1bc4266e4a70d4a34",
-            "sample1_mature_hairpin.sorted.stats:md5,c629c34adcbc081fd10a6792b93012bb",
+            "sample2_mature_hairpin.sorted.stats:md5,f5e8be4ea1e9f85c5dc15d3f8cdbae47",
+            "sample1_mature_hairpin.sorted.stats:md5,052c1f774377058033a165f05d2fcbec",
             "sample3_mature_hairpin.sorted.idxstats:md5,8927231d0ea3100fb75a96b4e5317321",
             "sample2_mature_hairpin.sorted.idxstats:md5,8927231d0ea3100fb75a96b4e5317321"
         ],
@@ -67,7 +67,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T15:20:57.561870232"
+        "timestamp": "2024-10-08T23:25:57.949148045"
     },
     "mirna_quant_edger_qc": {
         "content": [
diff --git a/tests/test_skipfastp.nf.test.snap b/tests/test_skipfastp.nf.test.snap
index ce2fdbd9..0484a8af 100644
--- a/tests/test_skipfastp.nf.test.snap
+++ b/tests/test_skipfastp.nf.test.snap
@@ -30,34 +30,34 @@
             "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,2620288b88bba1ea3315414016c083a1",
             "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,e0e4a95f5c21a926f7894cf1fbe3110b",
             "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,62208acf0c7418d590b41318d7e17d67",
-            "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,1c03f98d16d2e418692d3227c8be2803",
-            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,e5aee4c4e099d5f4e82bd22f58309e2c"
+            "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,c9d4d7a91bdafdb45592574cd942a7ba",
+            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,3309ee9de501160337af8c73d46ec682"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T20:19:25.61285999"
+        "timestamp": "2024-10-08T23:28:49.376604167"
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.4.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-02T13:45:55.267854723"
+        "timestamp": "2024-10-08T23:28:49.241105443"
     },
     "mirna_quant_bam": {
         "content": [
             "Clone1_N3_mature_hairpin.sorted.flagstat:md5,1630edf055b591303d7c68d013745938",
             true,
-            "Clone1_N3_mature_hairpin.sorted.stats:md5,b41149b9cb862c46d60ef21498f29e40",
+            "Clone1_N3_mature_hairpin.sorted.stats:md5,488f860e7aed290a4707dbe9b07899b6",
             true,
             "Clone1_N3_mature_hairpin.sorted.idxstats:md5,b44fb26f6be2accc7d52bc38efff69f4",
             true,
-            "Clone1_N3_mature.sorted.stats:md5,b1e54f83ae8a387a2071eda43ef3f9cb",
+            "Clone1_N3_mature.sorted.stats:md5,5263c781ef5db00ba664745ed595841f",
             true,
             true,
             true,
@@ -68,7 +68,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T15:26:42.634182624"
+        "timestamp": "2024-10-08T23:28:49.30034837"
     },
     "mirna_quant_edger_qc": {
         "content": [
diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap
index f56e3ff3..77c7af70 100644
--- a/tests/test_umi.nf.test.snap
+++ b/tests/test_umi.nf.test.snap
@@ -30,37 +30,37 @@
             "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc",
             "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873",
             "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad",
-            "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,6beddbebbd48d4ffc01e059c73a5a330",
-            "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,cc5ef7cbd5a29794170ac6cff59dfd76"
+            "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,f1ff3ed8478070d92f068c10bc2c1222",
+            "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,a058de81d9a8055bc40e345ae2ed660c"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-01T20:24:14.961610878"
+        "timestamp": "2024-10-08T23:34:54.845245469"
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_MATURE={bowtie=1.3.0, samtools=1.16.1}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.0, samtools=1.16.1}, CSVTK_JOIN={csvtk=0.30.0}, DATATABLE_MERGE={r-base=3.6.2}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.0}, INDEX_MATURE={bowtie=1.3.0}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.21}, SAMTOOLS_IDXSTATS={samtools=1.21}, SAMTOOLS_INDEX={samtools=1.21}, SAMTOOLS_SORT={samtools=1.21}, SAMTOOLS_STATS={samtools=1.21}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.4.0}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-10-02T13:51:36.160803304"
+        "timestamp": "2024-10-08T23:34:54.715037951"
     },
     "mirna_quant_bam": {
         "content": [
-            "SRX8195118_SRR11631014_mature.sorted.stats:md5,a49f7118b3cba5e304cf018089cefc8e",
+            "SRX8195118_SRR11631014_mature.sorted.stats:md5,d2e3a471dc1948dd546015623e4347f9",
             "SRX8195118_SRR11631014_mature.sorted.flagstat:md5,57c6d477394d367ebae59f7267b430a5",
             "SRX8195118_SRR11631014_mature.sorted.idxstats:md5,8b9cf0f1647b938f058b80522df24667",
-            "SRX8195117_SRR11631013_mature.sorted.stats:md5,6847689129964daf73e845cd5ee086db",
+            "SRX8195117_SRR11631013_mature.sorted.stats:md5,e489a85f4bf467724d7841d7e843a224",
             "SRX8195117_SRR11631013_mature.sorted.flagstat:md5,171387fb18ba9868e28ca03d24a7daca",
             "SRX8195117_SRR11631013_mature.sorted.idxstats:md5,fb6c4000f82a66654b4f2a40570649b5",
             "SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats:md5,4e7c1c98804febf6210cee5e3941709e",
             "SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat:md5,b86bd14dc687a26ba5a84d1015f4b70a",
-            "SRX8195117_SRR11631013_mature_hairpin.sorted.stats:md5,c7d9fb0a872991e46fecdd941085ed9e",
-            "SRX8195118_SRR11631014_mature_hairpin.sorted.stats:md5,168c0b770fc77bf9a7f85085aceff75a",
+            "SRX8195117_SRR11631013_mature_hairpin.sorted.stats:md5,b5d4e6934c5c07ace5ad9a7a4eeade08",
+            "SRX8195118_SRR11631014_mature_hairpin.sorted.stats:md5,990e41b7818b98083463b3bcd9862283",
             "SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats:md5,f4485713620f31d97a5006acdf6d8a5d",
             "SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat:md5,e0c44533bc7813d552de4864d997c916"
         ],
@@ -68,7 +68,7 @@
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T15:35:36.685710047"
+        "timestamp": "2024-10-08T23:34:54.777375775"
     },
     "mirna_quant_edger_qc": {
         "content": [