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multiqc_config.yaml 2.53 KB
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report_comment: >
    This report has been generated by the <a href="https://forgemia.inra.fr/genotoul-bioinfo/metagwgs" target="_blank">genotoul-bioinfo/metagwgs</a>
    analysis pipeline. For information about how to interpret these results, please see the
    <a href="https://forgemia.inra.fr/genotoul-bioinfo/metagwgs" target="_blank">documentation</a>.
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extra_fn_clean_trim:
  - "cleaned_"
  - "raw_"
  - '_kept_contigs'
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  - '.count_reads_on_contigs'
  - '.no_filter'
  - '.host_filter'
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  - '_scaffolds'
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  - '.txt'
  - '.contigs'
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  - '.sort'
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  - '_kaiju_MEM_verbose'
  - '_sickle'
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extra_fn_clean_exts:
  - "_select_contigs_cpm"
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module_order:
    - fastqc:
        name: 'FastQC (raw)'
        path_filters_exclude:
            - '*cleaned_*.zip'
    - cutadapt
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    - sickle:
        path_filters:
            - '*_sickle.log'
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    - samtools:
        name : 'Reads before host reads filter'
        info: 'This section reports of the reads alignement against host genome with bwa.(not sure to be interesting ????)'
        path_filters:
            - '*.no_filter.flagstat'
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    - samtools:
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        name : 'Reads aln on host genome'
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        info: 'This section of the cleaned reads alignement against host genome with bwa.'
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        path_filters:
            - '*host_filter/*'
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    - samtools:
        name : 'Reads after host reads filter'
        info: 'This section reports of the cleaned reads alignement against host genome with bwa.(not sure to be interesting ????)'
        path_filters:
            - '*.host_filter.flagstat'
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    - fastqc:
        name: 'FastQC (cleaned)'
        info: 'This section of the report shows FastQC results after adapter trimming and cleaning.'
        path_filters:
            - '*cleaned_*.zip'
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    - kaiju
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    - quast:
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        name: 'Quast primary assembly'
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        info: 'This section of the report shows quast results after assembly'
        path_filters:
            - '*_all_contigs_QC/*'
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    - quast:
        name: 'Quast filtered assembly'
        info: 'This section of the report shows quast results after filtering of assembly'
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        path_filters:
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            - '*_select_contigs_QC/*'
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    - samtools:
        name : 'Reads after deduplication'
        info: 'This section reports of deduplicated reads alignement against contigs with bwa.'
        path_filters:
            - '*.count_reads_on_contigs.flagstat'
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    - prokka
    - featureCounts
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prokka_fn_snames: True
prokka_table: True

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featurecounts:
  fn: '*.summary'
  shared: true
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table_columns_visible:
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  FastQC (raw):
        percent_duplicates: False
        percent_gc: False