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TCLamnidisTCLamnidis
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update snapshots
1 parent 2516316 commit c40bb9e

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Lines changed: 486 additions & 32 deletions

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‎tests/default.nf.test.snap‎

Lines changed: 139 additions & 8 deletions
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@@ -198,7 +198,6 @@
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause.bowtie2out.txt",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_profile.txt",
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"metaphlan_taxpasta_table.tsv",
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"BETA-multiqc.parquet",
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"ar_length_count_plot_All.txt",
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"ar_length_count_plot_Collapsed.txt",
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"ar_length_count_plot_Collapsed_Truncated.txt",
@@ -228,11 +227,13 @@
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"fiveprime_misinc_plot.txt",
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"length-distribution-Forward.txt",
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"length-distribution-Reverse.txt",
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"llms-full.txt",
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"mapdamage-fiveprime_misinc_plot.txt",
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"mapdamage-length-distribution-Forward.txt",
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"mapdamage-length-distribution-Reverse.txt",
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"mapdamage-threeprime_misinc_plot.txt",
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"multiqc.log",
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"multiqc.parquet",
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"multiqc_adapter_removal.txt",
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"multiqc_bcftools_stats.txt",
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"multiqc_citations.txt",
@@ -415,10 +416,10 @@
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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"nf-test": "0.9.3",
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"nextflow": "25.04.8"
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},
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"timestamp": "2025-09-11T14:23:20.334595"
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"timestamp": "2025-11-07T10:22:21.984388"
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},
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"read_filtering": {
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"content": [
@@ -461,6 +462,135 @@
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},
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"timestamp": "2025-05-02T18:37:30.913859"
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},
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"Test `test` profile:": {
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"content": [
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{
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"ADAPTERREMOVAL_PAIRED": {
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"adapterremoval": "2.3.2"
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},
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"ADAPTERREMOVAL_SINGLE": {
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"adapterremoval": "2.3.2"
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},
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"BCFTOOLS_INDEX_UG": {
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"bcftools": 1.18
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},
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"BCFTOOLS_STATS_GENOTYPING": {
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"bcftools": 1.18
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},
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"BUILD_INTERVALS": {
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"gawk": "5.1.0"
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},
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"BWA_ALN": {
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"bwa": "0.7.18-r1243-dirty"
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},
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"BWA_INDEX": {
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"bwa": "0.7.18-r1243-dirty"
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},
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"DAMAGEPROFILER": {
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"damageprofiler": 1.1
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},
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"ENDORSPY": {
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"endorspy": 1.3
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},
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"FASTQC": {
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"fastqc": "0.12.1"
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},
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"FASTQC_PROCESSED": {
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"fastqc": "0.12.1"
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},
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"FILTER_BAM_FRAGMENT_LENGTH": {
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"python": "3.9.15",
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"pysam": "0.20.0"
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},
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"GATK_INDELREALIGNER": {
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"gatk": "3.5-0-g36282e4"
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},
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"GATK_REALIGNERTARGETCREATOR": {
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"gatk": "3.5-0-g36282e4"
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},
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"GATK_UNIFIEDGENOTYPER": {
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"gatk": "3.5-0-g36282e4"
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},
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"METAPHLAN_METAPHLAN": {
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"metaphlan": "4.0.6"
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},
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"PICARD_CREATESEQUENCEDICTIONARY": {
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"picard": "3.1.1"
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},
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"PICARD_MARKDUPLICATES": {
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"picard": "3.1.1"
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},
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"PRESEQ_CCURVE": {
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"preseq": "3.1.1"
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},
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"QUALIMAP_BAMQC_NOBED": {
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"qualimap": 2.3
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},
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"SAMTOOLS_FAIDX": {
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"samtools": 1.18
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},
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"SAMTOOLS_FASTQ_METAGENOMICS": {
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"samtools": 1.18
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},
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"SAMTOOLS_FILTER_INDEX": {
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"samtools": 1.18
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},
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"SAMTOOLS_FLAGSTAT_DEDUPPED": {
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"samtools": 1.18
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},
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"SAMTOOLS_FLAGSTAT_FILTERED": {
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"samtools": 1.18
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},
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"SAMTOOLS_FLAGSTAT_MERGED_LIBRARIES": {
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"samtools": 1.18
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},
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"SAMTOOLS_INDEX": {
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"samtools": 1.18
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},
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"SAMTOOLS_INDEX_BAM_INPUT": {
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"samtools": 1.18
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},
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"SAMTOOLS_INDEX_DEDUPPED": {
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"samtools": 1.18
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},
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"SAMTOOLS_INDEX_MERGED_LIBRARIES": {
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"samtools": 1.18
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},
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"SAMTOOLS_LENGTH_FILTER_INDEX": {
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"samtools": 1.18
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},
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"SAMTOOLS_MERGE_DEDUPPED": {
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"samtools": 1.18
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},
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"SAMTOOLS_MERGE_LIBRARIES": {
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"samtools": 1.18
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},
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"SAMTOOLS_SORT_DEDUPPED": {
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"samtools": 1.18
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},
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"SAMTOOLS_SORT_MERGED_LIBRARIES": {
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"samtools": 1.18
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},
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"SAMTOOLS_VIEW": {
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"samtools": 1.18
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},
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"SAMTOOLS_VIEW_BAM_FILTERING": {
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"samtools": 1.18
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},
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"SEQKIT_SPLIT2": {
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"seqkit": "2.1.0"
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},
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"Workflow": {
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"nf-core/eager": "v3.0.0dev"
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}
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}
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],
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"meta": {
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"nf-test": "0.9.3",
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"nextflow": "25.04.8"
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},
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"timestamp": "2025-11-07T10:31:40.88452"
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},
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"preprocessing": {
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"content": [
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[
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"multiqc": {
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"content": [
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[
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"BETA-multiqc.parquet",
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"ar_length_count_plot_All.txt",
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"ar_length_count_plot_Collapsed.txt",
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"ar_length_count_plot_Collapsed_Truncated.txt",
@@ -600,11 +729,13 @@
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"fiveprime_misinc_plot.txt",
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"length-distribution-Forward.txt",
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"length-distribution-Reverse.txt",
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"llms-full.txt",
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"mapdamage-fiveprime_misinc_plot.txt",
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"mapdamage-length-distribution-Forward.txt",
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"mapdamage-length-distribution-Reverse.txt",
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"mapdamage-threeprime_misinc_plot.txt",
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"multiqc.log",
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"multiqc.parquet",
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"multiqc_adapter_removal.txt",
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"multiqc_bcftools_stats.txt",
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"multiqc_citations.txt",
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]
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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"nf-test": "0.9.3",
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"nextflow": "25.04.8"
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},
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"timestamp": "2025-09-11T14:23:20.798039"
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"timestamp": "2025-11-07T10:22:22.307696"
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},
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"mapping_output": {
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"content": [

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