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TCLamnidisTCLamnidis
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Merge branch 'dev' into nf-test-humanpopgen
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‎tests/test_minimal.nf.test‎

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nextflow_pipeline {
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name "Test pipeline: NFCORE_EAGER"
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script "main.nf"
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tag "pipeline"
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tag "nfcore_eager"
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tag "test_minimal"
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test("test_minimal_profile") {
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when {
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params {
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outdir = "$outputDir"
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}
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}
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then {
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///////////////////
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// DOCUMENTATION //
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///////////////////
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// The contents of each top level results directory should be tested with individually named snapshots.
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// Within each snapshot, there should be two to three distinct variables, that contain the files to be tested.
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// - stable_name_<dir> is for files with variable md5sums (i.e. content) so only names will be compared
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// - stable_content_<dir> is for files with stable md5sums (i.e. content) so md5sums will be compared
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// - bams_<dir> is for BAM files, where the headerMD5 is checked for stability (since the content can be unstable)
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// If a directory is fully stable, you can drop `stable_name_*`
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// If a directory contains no BAMs, you can drop `bams_*`
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// Generate with: nf-test test --tag test_minimal --profile docker,test_minimal --update-snapshot
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// Test with: nf-test test --tag test_minimal --profile docker,test_minimal
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// NOTE: BAMs are always only stable in name, because:
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// a) sharding breaks header since the shard that was first is named in the header (Fixed in https://github.com/nf-core/eager/pull/1112)
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// b) the order of the reads in the BAMs is not stable (sorted, but reads that share a start position can be in any order)
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// point b) also causes BAIs to be unstable.
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// c) Merging of multiple BAMs with duplicate @RG / @PG tags can cause the header to be unstable (particularly in the case of shards/lanes)
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//////////////////////
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// DEFINE VARIABLES //
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//////////////////////
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// Define exclusion patterns for files with unstable contents
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// NOTE: When a section needs more than a couple of small patterns, consider adding a variable to store the patterns here
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// This is particularly important if the patterns excluded in the stable content section should be included in the stable name section
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// Check that no files are missing/added
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// Command legend: Result directory to index , includeDir: include dirs?, ignore: exclude patterns , ignoreFile: exclude pattern list , include: include patterns
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def stable_name_all = getAllFilesFromDir("$outputDir/" , includeDir: false , ignore: ['pipeline_info/*'] , ignoreFile: null , include: ['*', '**/*'] )
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// Authentication
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def stable_content_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )
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// def stable_name_authentication = getAllFilesFromDir("$outputDir/authentication" , includeDir: false , ignore: null , ignoreFile: null , include: unstable_patterns_auth)
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// Final_bams
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def stable_content_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_final_bams = getAllFilesFromDir("$outputDir/final_bams" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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// Mapping (incl. bam_input flasgstat)
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def stable_content_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.flagstat'] )
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def stable_name_mapping = getAllFilesFromDir("$outputDir/mapping" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{bam,bai}'] )
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// Preprocessing
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def stable_content_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: ['**/*.{zip,html}'] , ignoreFile: null , include: ['**/*'] )
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def stable_name_preprocessing = getAllFilesFromDir("$outputDir/preprocessing" , includeDir: false , ignore: null , ignoreFile: null , include: ['**/*.{zip,html}'] )
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// MultiQC
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def stable_name_multiqc = getAllFilesFromDir("$outputDir/multiqc" , includeDir: false , ignore: null , ignoreFile: null , include: ['*', '**/*'] )
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///////////////////////
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// DEFINE ASSERTIONS //
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///////////////////////
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assertAll(
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{ assert workflow.success },
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// This checks that there are no missing or additional output files.
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// Also a good starting point to look at all the files in the output folder than need to be checked in subsequent sections.
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{ assert snapshot( stable_name_all*.name ).match("all_files") },
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// Checking changes to contents of each section
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// NOTE: Keep the order of the sections in the alphanumeric order of the output directories.
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// Each section should first check stable_content, stable_name second (if applicable).
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{ assert snapshot( stable_content_authentication ).match("authentication") },
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{ assert snapshot( stable_content_final_bams , stable_name_final_bams*.name ).match("final_bams") },
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// NOTE: The snapshot section for mapping cannot be named 'mapping'. See https://github.com/askimed/nf-test/issues/279
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{ assert snapshot( stable_content_mapping , stable_name_mapping*.name ).match("mapping_output") },
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{ assert snapshot( stable_content_preprocessing , stable_name_preprocessing*.name ).match("preprocessing") },
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// MultiQC
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{ assert snapshot( stable_name_multiqc*.name ).match("multiqc") },
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// Versions
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{ assert new File("$outputDir/pipeline_info/nf_core_eager_software_mqc_versions.yml").exists() },
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)
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}
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}
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}

‎tests/test_minimal.nf.test.snap‎

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{
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"all_files": {
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"content": [
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[
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json",
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"JK2782_Mammoth_MT_Krause.bam",
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"JK2782_Mammoth_MT_Krause.bam.bai",
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"JK2802_Mammoth_MT_Krause.bam",
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"JK2802_Mammoth_MT_Krause.bam.bai",
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"JK2782_Mammoth_MT_Krause.flagstat",
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"JK2802_Mammoth_MT_Krause.flagstat",
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.flagstat",
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam",
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam.bai",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat",
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"fastqc-status-check-heatmap.txt",
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"fastqc_adapter_content_plot.txt",
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"fastqc_per_base_n_content_plot.txt",
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"fastqc_per_base_sequence_quality_plot.txt",
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"fastqc_per_sequence_gc_content_plot_Counts.txt",
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"fastqc_per_sequence_gc_content_plot_Percentages.txt",
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"fastqc_per_sequence_quality_scores_plot.txt",
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"fastqc_sequence_counts_plot.txt",
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"fastqc_sequence_duplication_levels_plot.txt",
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"fastqc_top_overrepresented_sequences_table.txt",
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"multiqc.log",
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"multiqc_citations.txt",
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"multiqc_data.json",
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"multiqc_fastqc.txt",
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"multiqc_general_stats.txt",
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"multiqc_samtools_flagstat.txt",
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"multiqc_software_versions.txt",
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"multiqc_sources.txt",
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"samtools-flagstat-dp_Percentage_of_total.txt",
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"samtools-flagstat-dp_Read_counts.txt",
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"fastqc-status-check-heatmap.pdf",
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"fastqc_adapter_content_plot.pdf",
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"fastqc_per_base_n_content_plot.pdf",
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"fastqc_per_base_sequence_quality_plot.pdf",
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"fastqc_per_sequence_gc_content_plot_Counts.pdf",
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"fastqc_per_sequence_gc_content_plot_Percentages.pdf",
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"fastqc_per_sequence_quality_scores_plot.pdf",
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"fastqc_sequence_counts_plot-cnt.pdf",
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"fastqc_sequence_counts_plot-pct.pdf",
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"fastqc_sequence_duplication_levels_plot.pdf",
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"fastqc_top_overrepresented_sequences_table.pdf",
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"general_stats_table.pdf",
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"samtools-flagstat-dp_Percentage_of_total.pdf",
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"samtools-flagstat-dp_Read_counts.pdf",
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"fastqc-status-check-heatmap.png",
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"fastqc_adapter_content_plot.png",
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"fastqc_per_base_n_content_plot.png",
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"fastqc_per_base_sequence_quality_plot.png",
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"fastqc_per_sequence_gc_content_plot_Counts.png",
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"fastqc_per_sequence_gc_content_plot_Percentages.png",
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"fastqc_per_sequence_quality_scores_plot.png",
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"fastqc_sequence_counts_plot-cnt.png",
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"fastqc_sequence_counts_plot-pct.png",
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"fastqc_sequence_duplication_levels_plot.png",
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"fastqc_top_overrepresented_sequences_table.png",
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"general_stats_table.png",
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"samtools-flagstat-dp_Percentage_of_total.png",
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"samtools-flagstat-dp_Read_counts.png",
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"fastqc-status-check-heatmap.svg",
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"fastqc_adapter_content_plot.svg",
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"fastqc_per_base_n_content_plot.svg",
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"fastqc_per_base_sequence_quality_plot.svg",
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"fastqc_per_sequence_gc_content_plot_Counts.svg",
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"fastqc_per_sequence_gc_content_plot_Percentages.svg",
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"fastqc_per_sequence_quality_scores_plot.svg",
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"fastqc_sequence_counts_plot-cnt.svg",
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"fastqc_sequence_counts_plot-pct.svg",
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"fastqc_sequence_duplication_levels_plot.svg",
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"fastqc_top_overrepresented_sequences_table.svg",
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"general_stats_table.svg",
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"samtools-flagstat-dp_Percentage_of_total.svg",
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"samtools-flagstat-dp_Read_counts.svg",
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"multiqc_report.html",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip",
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"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html",
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"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.672625"
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},
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"preprocessing": {
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"content": [
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[
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],
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[
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"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.html",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_1_fastqc.zip",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.html",
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"JK2782_JK2782_TGGCCGATCAACGA_L1_2_fastqc.zip",
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"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.html",
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"JK2802_JK2802_AGAATAACCTACCA_L2_fastqc.zip"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.803481"
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},
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"final_bams": {
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"content": [
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[
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"JK2782_Mammoth_MT_Krause.flagstat:md5,9ebb4b5e99894d2a87ac3b60a78e7142",
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"JK2802_Mammoth_MT_Krause.flagstat:md5,51816d63f34b4818ed6f1ec968f05fc0"
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],
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[
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"JK2782_Mammoth_MT_Krause.bam",
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"JK2782_Mammoth_MT_Krause.bam.bai",
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"JK2802_Mammoth_MT_Krause.bam",
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"JK2802_Mammoth_MT_Krause.bam.bai"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.749353"
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},
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"multiqc": {
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"content": [
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[
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"fastqc-status-check-heatmap.txt",
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"fastqc_adapter_content_plot.txt",
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"fastqc_per_base_n_content_plot.txt",
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"fastqc_per_base_sequence_quality_plot.txt",
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"fastqc_per_sequence_gc_content_plot_Counts.txt",
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"fastqc_per_sequence_gc_content_plot_Percentages.txt",
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"fastqc_per_sequence_quality_scores_plot.txt",
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"fastqc_sequence_counts_plot.txt",
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"fastqc_sequence_duplication_levels_plot.txt",
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"fastqc_top_overrepresented_sequences_table.txt",
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"multiqc.log",
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"multiqc_citations.txt",
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"multiqc_data.json",
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"multiqc_fastqc.txt",
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"multiqc_general_stats.txt",
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"multiqc_samtools_flagstat.txt",
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"multiqc_software_versions.txt",
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"multiqc_sources.txt",
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"samtools-flagstat-dp_Percentage_of_total.txt",
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"samtools-flagstat-dp_Read_counts.txt",
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"fastqc-status-check-heatmap.pdf",
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"fastqc_adapter_content_plot.pdf",
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"fastqc_per_base_n_content_plot.pdf",
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"fastqc_per_base_sequence_quality_plot.pdf",
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"fastqc_per_sequence_gc_content_plot_Counts.pdf",
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"fastqc_per_sequence_gc_content_plot_Percentages.pdf",
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"fastqc_per_sequence_quality_scores_plot.pdf",
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"fastqc_sequence_counts_plot-cnt.pdf",
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"fastqc_sequence_counts_plot-pct.pdf",
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"fastqc_sequence_duplication_levels_plot.pdf",
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"fastqc_top_overrepresented_sequences_table.pdf",
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"general_stats_table.pdf",
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"samtools-flagstat-dp_Percentage_of_total.pdf",
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"samtools-flagstat-dp_Read_counts.pdf",
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"fastqc-status-check-heatmap.png",
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"fastqc_adapter_content_plot.png",
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"fastqc_per_base_n_content_plot.png",
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"fastqc_per_base_sequence_quality_plot.png",
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"fastqc_per_sequence_gc_content_plot_Counts.png",
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"fastqc_per_sequence_gc_content_plot_Percentages.png",
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"fastqc_per_sequence_quality_scores_plot.png",
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"fastqc_sequence_counts_plot-cnt.png",
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"fastqc_sequence_counts_plot-pct.png",
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"fastqc_sequence_duplication_levels_plot.png",
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"fastqc_top_overrepresented_sequences_table.png",
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"general_stats_table.png",
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"samtools-flagstat-dp_Percentage_of_total.png",
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"samtools-flagstat-dp_Read_counts.png",
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"fastqc-status-check-heatmap.svg",
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"fastqc_adapter_content_plot.svg",
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"fastqc_per_base_n_content_plot.svg",
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"fastqc_per_base_sequence_quality_plot.svg",
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"fastqc_per_sequence_gc_content_plot_Counts.svg",
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"fastqc_per_sequence_gc_content_plot_Percentages.svg",
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"fastqc_per_sequence_quality_scores_plot.svg",
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"fastqc_sequence_counts_plot-cnt.svg",
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"fastqc_sequence_counts_plot-pct.svg",
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"fastqc_sequence_duplication_levels_plot.svg",
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"fastqc_top_overrepresented_sequences_table.svg",
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"general_stats_table.svg",
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"samtools-flagstat-dp_Percentage_of_total.svg",
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"samtools-flagstat-dp_Read_counts.svg",
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"multiqc_report.html"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.824552"
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},
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"mapping_output": {
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"content": [
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[
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.flagstat:md5,9a10991f5670a52975a622a8b056e2bc",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.flagstat:md5,274942e6f459e1f85bffd0719ea24038",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.flagstat:md5,51816d63f34b4818ed6f1ec968f05fc0"
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],
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[
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam",
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_sorted.bam.bai",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_sorted.bam.bai",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_sorted.bam.bai"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.771636"
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},
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"authentication": {
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"content": [
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[
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"JK2782_JK2782_TGGCCGATCAACGA_BAM_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,13303511f19f618a524e30b3377497fb",
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"JK2782_JK2782_TGGCCGATCAACGA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,90a8f1d5c1017f0000ac960b03767eba",
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"JK2802_JK2802_AGAATAACCTACCA_Mammoth_MT_Krause_percent_on_target_mqc.json:md5,d26aac162887528fb3a3b2fa9b86954f"
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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": "24.10.6"
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},
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"timestamp": "2025-05-23T10:36:48.717265"
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}
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}

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