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test: update tests snapshots
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‎tests/test_contamination_tech_reps.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{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}}"
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"{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}, 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}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, 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}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-08T23:16:26.853242481"
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"timestamp": "2024-12-10T00:29:32.052341"
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},
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"mirna_quant_bam": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:04.974546479"
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"timestamp": "2024-12-10T00:29:32.116301175"
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},
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"mirna_quant_edger_qc": {
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:05.025175321"
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"timestamp": "2024-12-10T00:29:32.164075991"
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},
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"contaminant_filter_filter": {
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"content": [
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-01T20:06:05.070939602"
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"timestamp": "2024-12-10T00:29:32.208602197"
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}
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}
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}

‎tests/test_mirgenedb.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{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}, 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}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, 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}}"
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"{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}, 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}, MIRDEEP2_MAPPER={mirdeep2=2.0.1}, MIRDEEP2_MIRDEEP2={mirdeep2=2.0.1}, MIRTOP_COUNTS={mirtop=0.4.28}, MIRTOP_EXPORT={mirtop=0.4.28}, MIRTOP_GFF={mirtop=0.4.28}, MIRTOP_STATS={mirtop=0.4.28}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, 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}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.10.0"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-11-11T13:44:14.583324793"
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"timestamp": "2024-12-10T00:35:18.448206326"
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"mirna_quant_bam": {
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"content": [

‎tests/test_nextflex.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{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}}"
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"{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}, 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}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, 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}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-08T23:25:57.880948228"
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"timestamp": "2024-12-10T00:37:47.333537716"
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"mirna_quant_bam": {
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"timestamp": "2024-09-20T17:11:24.369706104"
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}
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}
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}

‎tests/test_skipfastp.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{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}}"
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"{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}, 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}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, 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}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-08T23:28:49.241105443"
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"timestamp": "2024-12-10T00:40:10.829696529"
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},
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"mirna_quant_bam": {
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"content": [
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},
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"timestamp": "2024-10-01T20:19:25.557700049"
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}
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}

‎tests/test_umi.nf.test.snap

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},
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"software_versions": {
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"content": [
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"{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}}"
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"{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}, 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}, PIVOT_LONGER={r-base=4.4.2, tidyr=1.3.1, optparse=1.7.5}, PIVOT_WIDER={r-base=4.4.2, tidyr=1.3.1, dplyr=1.1.4, optparse=1.7.5, vroom=1.6.5}, 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}}"
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.04.4"
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"nextflow": "24.10.2"
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},
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"timestamp": "2024-10-08T23:34:54.715037951"
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"timestamp": "2024-12-10T00:44:45.433524507"
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},
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"mirna_quant_bam": {
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"content": [
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},
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"timestamp": "2024-09-20T19:12:28.290360163"
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}
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}
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}

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