diff --git a/tests/test_contamination_tech_reps.nf.test.snap b/tests/test_contamination_tech_reps.nf.test.snap
index 5ab7bf35..84b93867 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}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, 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}, MAP_CDNA={bowtie2=2.4.5}, MAP_NCRNA={bowtie2=2.4.5}, MAP_TRNA={bowtie2=2.4.5}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, SEQKIT_GREP_CDNA={seqkit=2.8.0}, SEQKIT_GREP_NCRNA={seqkit=2.8.0}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BLAT_CDNA={blat=36}, BLAT_NCRNA={blat=36}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, 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}, MAP_CDNA={bowtie2=2.4.5}, MAP_NCRNA={bowtie2=2.4.5}, MAP_TRNA={bowtie2=2.4.5}, MIRTOP_COUNTS={mirtop=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, 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}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T19:02:52.291291541"
+        "timestamp": "2024-09-20T13:27:35.553235807"
     },
     "mirna_quant_bam": {
         "content": [
diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap
index 1a073de6..b8ea7f91 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:md5,921509048d1cb44420cf8c6e6c8d0b49",
+            "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,201486e8c88b0dbb639776f9dacefe66",
             "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,aa37c5da7c2b4505ce58c3a21f97121c",
-            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,2ee0052e61923ba4250901319dce2bb3",
-            "Control_N1_mature_hairpin_genome.sorted.stats:md5,1dd143f511b43a4972e1533766c6e15c",
+            "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,5679af445f4628e0f4137f339319c950",
+            "Control_N1_mature_hairpin_genome.sorted.stats:md5,4da4f877f06083f616a0d76edd04ea22",
             "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": "2024-09-19T18:24:33.315499208"
+        "timestamp": "2024-09-20T13:36:32.067039888"
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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}, 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}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T18:24:33.252062081"
+        "timestamp": "2024-09-20T13:36:31.98986503"
     },
     "mirna_quant_bam": {
         "content": [
diff --git a/tests/test_nextflex.nf.test.snap b/tests/test_nextflex.nf.test.snap
index 63e7a361..7148520f 100644
--- a/tests/test_nextflex.nf.test.snap
+++ b/tests/test_nextflex.nf.test.snap
@@ -34,13 +34,13 @@
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, 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}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T19:56:32.088274453"
+        "timestamp": "2024-09-20T13:40:20.532779636"
     },
     "mirna_quant_bam": {
         "content": [
diff --git a/tests/test_skipfastp.nf.test.snap b/tests/test_skipfastp.nf.test.snap
index 1cae9547..098f0e35 100644
--- a/tests/test_skipfastp.nf.test.snap
+++ b/tests/test_skipfastp.nf.test.snap
@@ -41,13 +41,13 @@
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, 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}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T20:03:31.119734675"
+        "timestamp": "2024-09-20T13:44:34.328354483"
     },
     "mirna_quant_bam": {
         "content": [
diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap
index b039be6e..2188d7b6 100644
--- a/tests/test_umi.nf.test.snap
+++ b/tests/test_umi.nf.test.snap
@@ -41,13 +41,13 @@
     },
     "software_versions": {
         "content": [
-            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, MIRTRACE_QC={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_COLLAPSE={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
+            "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, 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=0.4.25}, MIRTOP_EXPORT={mirtop=0.4.25}, MIRTOP_GFF={mirtop=0.4.25}, MIRTOP_STATS={mirtop=0.4.25}, 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}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-09-19T20:12:37.506078835"
+        "timestamp": "2024-09-20T13:50:10.366114108"
     },
     "mirna_quant_bam": {
         "content": [