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Joon-KlapsJoon-Klaps
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spades update & version bumps
1 parent 35c1e25 commit 0054c87

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-127
lines changed

‎.nf-core.yml

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bump_version: null
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bump_version:
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nf_core_version: 3.1.0
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org_path: null
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org_path:
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repository_type: pipeline
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lint:
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files_unchanged:
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actions_ci: false
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template:
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name: viralgenie
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description: a bioinformatics best-practice analysis pipeline for reconstructing consensus genomes and to identify intra-host variants from metagenomic sequencing data or enriched based sequencing data like hybrid capture.
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description: a bioinformatics best-practice analysis pipeline for reconstructing
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consensus genomes and to identify intra-host variants from metagenomic sequencing
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data or enriched based sequencing data like hybrid capture.
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author: "Joon Klaps, Philippe Lemey, Liana Kafetzopoulou"
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is_nfcore: false
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org: Joon-Klaps
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skip_features:
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- igenomes
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force: false
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outdir: .
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version: 0.1.1dev
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update: null
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version: 0.1.2
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update:

‎assets/multiqc_config.yml

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report_comment: >
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This report has been generated by the <a href="https://github.com/Joon-Klaps/viralgenie/dev/" target="_blank">Joon-Klaps/viralgenie</a>
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analysis pipeline. For information about how to interpret these results, please see the
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<a href="https://joon-klaps.github.io/viralgenie/latest/dev/usage/" target="_blank">documentation</a>.
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This report has been generated by the <a href="https://github.com/Joon-Klaps/viralgenie/0.1.2/"
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target="_blank">Joon-Klaps/viralgenie</a> analysis pipeline. For information about
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how to interpret these results, please see the <a href="https://joon-klaps.github.io/viralgenie/latest/0.1.2/usage/"
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target="_blank">documentation</a>.
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export_plots: true
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data_format: "yaml"
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# Summary table visible columns
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table_columns_visible:
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"SAMPLE: FastQC (pre-Trimming)":
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total_sequences: True
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avg_sequence_length: True
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percent_gc: False
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percent_duplicates: False
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percent_fails: False
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total_sequences: true
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avg_sequence_length: true
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percent_gc: false
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percent_duplicates: false
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percent_fails: false
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"SAMPLE: FastQC (post-Trimming)":
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total_sequences: True
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avg_sequence_length: True
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percent_gc: True
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percent_duplicates: True
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percent_fails: True
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total_sequences: true
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avg_sequence_length: true
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percent_gc: true
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percent_duplicates: true
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percent_fails: true
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"SAMPLE: FastQC (post-Host-removal)":
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total_sequences: True
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avg_sequence_length: True
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percent_gc: True
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percent_duplicates: True
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percent_fails: True
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total_sequences: true
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avg_sequence_length: true
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percent_gc: true
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percent_duplicates: true
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percent_fails: true
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"SAMPLE: fastp":
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filtering_result_passed_filter_reads: False
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after_filtering_q30_rate: True
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"CLUSTER: Samtools Stats: stats": False
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"CLUSTER: Samtools Stats: flagstat": False
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"CLUSTER: Bcftools: Stats": False
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"CLUSTER: Samtools Stats": False
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"CLUSTER: Picard: Mark Duplicates": False
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"CLUSTER: UMI-tools": False
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"CLUSTER: mosdepth": False
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filtering_result_passed_filter_reads: false
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after_filtering_q30_rate: true
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"CLUSTER: Samtools Stats: stats": false
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"CLUSTER: Samtools Stats: flagstat": false
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"CLUSTER: Bcftools: Stats": false
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"CLUSTER: Samtools Stats": false
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"CLUSTER: Picard: Mark Duplicates": false
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"CLUSTER: UMI-tools": false
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"CLUSTER: mosdepth": false
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"SAMPLE: BBduk":
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Total Removed bases percent: False
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Total Removed reads percent: True
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Total Removed reads: True
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Total Removed bases percent: false
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Total Removed reads percent: true
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Total Removed reads: true
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"SAMPLE: Quast (Spades)":
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N50: True
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L50: False
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Largest contig: True
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Total length: False
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N50: true
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L50: false
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Largest contig: true
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Total length: false
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"SAMPLE: Quast (Megahit)":
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N50: True
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L50: False
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Largest contig: True
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Total length: False
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N50: true
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L50: false
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Largest contig: true
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Total length: false
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"SAMPLE: Quast (Trinity)":
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N50: True
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L50: False
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Largest contig: True
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Total length: False
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N50: true
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L50: false
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Largest contig: true
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Total length: false
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# Viral reads are not so big
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read_count_multiplier: 1

‎modules.json

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},
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"spades": {
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"branch": "master",
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"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
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"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
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"installed_by": ["modules"]
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},
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"tabix/tabix": {

‎modules/local/blast_filter/environment.yml

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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- conda-forge::bioframe=0.4.1
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- conda-forge::pandas=2.2.3
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- pip
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- pip:
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- biopython==1.85

‎modules/local/blast_filter/main.nf

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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-949aaaddebd054dc6bded102520daff6f0f93ce6:aa2a3707bfa0550fee316844baba7752eaab7802-0':
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'biocontainers/mulled-v2-949aaaddebd054dc6bded102520daff6f0f93ce6:aa2a3707bfa0550fee316844baba7752eaab7802-0' }"
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'community.wave.seqera.io/library/pandas_pip_biopython:465ab8e47f7a0510' }"
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input:
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tuple val(meta), path(blast)
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tuple val(meta), path(contigs)
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tuple val(meta2), path(db)
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tuple val(meta2), path(contigs)
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tuple val(meta3), path(db)
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output:
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tuple val(meta), path("*.hits.txt") , emit: hits, optional: true

‎modules/local/network_cluster/environment.yml

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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- conda-forge::leidenalg=0.10.1
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- conda-forge::python-igraph=0.11.3

‎modules/local/select_reference/environment.yml

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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- conda-forge::bioframe=0.4.1
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- conda-forge::pandas=2.2.3
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- pip
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- pip:
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- biopython==1.85

‎modules/local/select_reference/main.nf

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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-949aaaddebd054dc6bded102520daff6f0f93ce6:aa2a3707bfa0550fee316844baba7752eaab7802-0':
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'biocontainers/mulled-v2-949aaaddebd054dc6bded102520daff6f0f93ce6:aa2a3707bfa0550fee316844baba7752eaab7802-0' }"
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'community.wave.seqera.io/library/pandas_pip_biopython:465ab8e47f7a0510' }"
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input:
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tuple val(meta), path(screen), path(reference), path(reads)

‎modules/nf-core/spades/environment.yml

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‎modules/nf-core/spades/main.nf

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