LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
multiqc/__init__.py
multiqc/__main__.py
multiqc/base_module.py
multiqc/config.py
multiqc/config_defaults.yaml
multiqc/interactive.py
multiqc/multiqc.py
multiqc/py.typed
multiqc/report.py
multiqc/search_patterns.yaml
multiqc/types.py
multiqc/validation.py
multiqc.egg-info/PKG-INFO
multiqc.egg-info/SOURCES.txt
multiqc.egg-info/dependency_links.txt
multiqc.egg-info/entry_points.txt
multiqc.egg-info/requires.txt
multiqc.egg-info/top_level.txt
multiqc/core/__init__.py
multiqc/core/exceptions.py
multiqc/core/exec_modules.py
multiqc/core/file_search.py
multiqc/core/log_and_rich.py
multiqc/core/order_modules_and_sections.py
multiqc/core/plugin_hooks.py
multiqc/core/software_versions.py
multiqc/core/strict_helpers.py
multiqc/core/tmp_dir.py
multiqc/core/update_config.py
multiqc/core/version_check.py
multiqc/core/write_results.py
multiqc/modules/__init__.py
multiqc/modules/profile_runtime.py
multiqc/modules/software_versions.py
multiqc/modules/adapterremoval/__init__.py
multiqc/modules/adapterremoval/adapterremoval.py
multiqc/modules/afterqc/__init__.py
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multiqc/modules/anglerfish/__init__.py
multiqc/modules/anglerfish/anglerfish.py
multiqc/modules/bakta/__init__.py
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multiqc/modules/bamtools/__init__.py
multiqc/modules/bamtools/bamtools.py
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multiqc/modules/bbduk/__init__.py
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multiqc/modules/bbmap/__init__.py
multiqc/modules/bbmap/bbmap.py
multiqc/modules/bbmap/bbmap_filetypes.py
multiqc/modules/bbmap/plot_aqhist.py
multiqc/modules/bbmap/plot_basic_hist.py
multiqc/modules/bbmap/plot_bhist.py
multiqc/modules/bbmap/plot_bqhist.py
multiqc/modules/bbmap/plot_covhist.py
multiqc/modules/bbmap/plot_idhist.py
multiqc/modules/bbmap/plot_ihist.py
multiqc/modules/bbmap/plot_indelhist.py
multiqc/modules/bbmap/plot_mhist.py
multiqc/modules/bbmap/plot_qahist.py
multiqc/modules/bbmap/plot_qchist.py
multiqc/modules/bbmap/plot_qhist.py
multiqc/modules/bcftools/__init__.py
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multiqc/modules/bcl2fastq/__init__.py
multiqc/modules/bcl2fastq/bcl2fastq.py
multiqc/modules/bclconvert/__init__.py
multiqc/modules/bclconvert/bclconvert.py
multiqc/modules/biobambam2/__init__.py
multiqc/modules/biobambam2/biobambam2.py
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multiqc/modules/biscuit/__init__.py
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multiqc/modules/bismark/__init__.py
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multiqc/modules/cellranger/__init__.py
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multiqc/modules/cellranger/count.py
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multiqc/modules/cellranger/vdj.py
multiqc/modules/checkqc/__init__.py
multiqc/modules/checkqc/checkqc.py
multiqc/modules/clipandmerge/__init__.py
multiqc/modules/clipandmerge/clipandmerge.py
multiqc/modules/clusterflow/__init__.py
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multiqc/modules/conpair/__init__.py
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multiqc/modules/cutadapt/__init__.py
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multiqc/modules/damageprofiler/__init__.py
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multiqc/modules/dedup/__init__.py
multiqc/modules/dedup/dedup.py
multiqc/modules/deeptools/__init__.py
multiqc/modules/deeptools/bamPEFragmentSizeDistribution.py
multiqc/modules/deeptools/bamPEFragmentSizeTable.py
multiqc/modules/deeptools/deeptools.py
multiqc/modules/deeptools/estimateReadFiltering.py
multiqc/modules/deeptools/plotCorrelation.py
multiqc/modules/deeptools/plotCoverage.py
multiqc/modules/deeptools/plotEnrichment.py
multiqc/modules/deeptools/plotFingerprint.py
multiqc/modules/deeptools/plotPCA.py
multiqc/modules/deeptools/plotProfile.py
multiqc/modules/diamond/__init__.py
multiqc/modules/diamond/diamond.py
multiqc/modules/disambiguate/__init__.py
multiqc/modules/disambiguate/disambiguate.py
multiqc/modules/dragen/__init__.py
multiqc/modules/dragen/coverage_hist.py
multiqc/modules/dragen/coverage_metrics.py
multiqc/modules/dragen/coverage_per_contig.py
multiqc/modules/dragen/dragen.py
multiqc/modules/dragen/dragen_gc_metrics.py
multiqc/modules/dragen/fragment_length.py
multiqc/modules/dragen/mapping_metrics.py
multiqc/modules/dragen/overall_mean_cov.py
multiqc/modules/dragen/ploidy_estimation_metrics.py
multiqc/modules/dragen/rna_quant_metrics.py
multiqc/modules/dragen/rna_transcript_cov.py
multiqc/modules/dragen/sc_atac_metrics.py
multiqc/modules/dragen/sc_rna_metrics.py
multiqc/modules/dragen/time_metrics.py
multiqc/modules/dragen/trimmer_metrics.py
multiqc/modules/dragen/utils.py
multiqc/modules/dragen/vc_metrics.py
multiqc/modules/dragen/tests/__init__.py
multiqc/modules/dragen/tests/test_dragen.py
multiqc/modules/dragen_fastqc/__init__.py
multiqc/modules/dragen_fastqc/base_metrics.py
multiqc/modules/dragen_fastqc/content_metrics.py
multiqc/modules/dragen_fastqc/dragen_fastqc.py
multiqc/modules/dragen_fastqc/gc_metrics.py
multiqc/modules/dragen_fastqc/read_metrics.py
multiqc/modules/dragen_fastqc/util.py
multiqc/modules/dragen_fastqc/assets/js/multiqc_dragen_fastqc.js
multiqc/modules/eigenstratdatabasetools/__init__.py
multiqc/modules/eigenstratdatabasetools/eigenstratdatabasetools.py
multiqc/modules/fastp/__init__.py
multiqc/modules/fastp/fastp.py
multiqc/modules/fastq_screen/__init__.py
multiqc/modules/fastq_screen/fastq_screen.py
multiqc/modules/fastqc/__init__.py
multiqc/modules/fastqc/fastqc.py
multiqc/modules/fastqc/assets/css/multiqc_fastqc.css
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multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_hg38_genome.txt
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_hg38_txome.txt
multiqc/modules/fastqc/fastqc_theoretical_gc/fastqc_theoretical_gc_mm10_genome.txt
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multiqc/modules/featurecounts/__init__.py
multiqc/modules/featurecounts/featurecounts.py
multiqc/modules/fgbio/__init__.py
multiqc/modules/fgbio/error_rate_by_read_position.py
multiqc/modules/fgbio/fgbio.py
multiqc/modules/fgbio/group_reads_by_umi.py
multiqc/modules/filtlong/__init__.py
multiqc/modules/filtlong/filtlong.py
multiqc/modules/flash/__init__.py
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multiqc/modules/flexbar/__init__.py
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multiqc/modules/freyja/__init__.py
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multiqc/modules/ganon/__init__.py
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multiqc/modules/gatk/__init__.py
multiqc/modules/gatk/analyze_saturation_mutagenesis.py
multiqc/modules/gatk/base_recalibrator.py
multiqc/modules/gatk/gatk.py
multiqc/modules/gatk/varianteval.py
multiqc/modules/gffcompare/__init__.py
multiqc/modules/gffcompare/gffcompare.py
multiqc/modules/glimpse/__init__.py
multiqc/modules/glimpse/err_grp.py
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multiqc/modules/goleft_indexcov/__init__.py
multiqc/modules/goleft_indexcov/goleft_indexcov.py
multiqc/modules/gopeaks/__init__.py
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multiqc/modules/haplocheck/__init__.py
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multiqc/modules/happy/__init__.py
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multiqc/modules/homer/__init__.py
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multiqc/modules/hostile/__init__.py
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multiqc/modules/jellyfish/__init__.py
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multiqc/modules/kaiju/__init__.py
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multiqc/modules/kallisto/__init__.py
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multiqc/modules/kraken/__init__.py
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multiqc/modules/leehom/__init__.py
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multiqc/modules/longranger/__init__.py
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multiqc/modules/macs2/__init__.py
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multiqc/modules/megahit/__init__.py
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multiqc/modules/metaphlan/__init__.py
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multiqc/modules/methylqa/__init__.py
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multiqc/modules/minionqc/__init__.py
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multiqc/modules/mirtop/__init__.py
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multiqc/modules/mirtrace/__init__.py
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multiqc/modules/mosdepth/__init__.py
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multiqc/modules/motus/__init__.py
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multiqc/modules/mtnucratio/__init__.py
multiqc/modules/mtnucratio/mtnucratio.py
multiqc/modules/multivcfanalyzer/__init__.py
multiqc/modules/multivcfanalyzer/multivcfanalyzer.py
multiqc/modules/nanoq/__init__.py
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multiqc/modules/nanostat/__init__.py
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multiqc/modules/nextclade/__init__.py
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multiqc/modules/ngsbits/__init__.py
multiqc/modules/ngsbits/mappingqc.py
multiqc/modules/ngsbits/ngsbits.py
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multiqc/modules/ngsbits/samplegender.py
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multiqc/modules/ngsderive/__init__.py
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multiqc/modules/nonpareil/__init__.py
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multiqc/modules/odgi/__init__.py
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multiqc/modules/pairtools/__init__.py
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multiqc/modules/phantompeakqualtools/__init__.py
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multiqc/modules/picard/AlignmentSummaryMetrics.py
multiqc/modules/picard/BaseDistributionByCycleMetrics.py
multiqc/modules/picard/CrosscheckFingerprints.py
multiqc/modules/picard/ExtractIlluminaBarcodes.py
multiqc/modules/picard/GcBiasMetrics.py
multiqc/modules/picard/HsMetrics.py
multiqc/modules/picard/IlluminaBasecallingMetrics.py
multiqc/modules/picard/IlluminaLaneMetrics.py
multiqc/modules/picard/InsertSizeMetrics.py
multiqc/modules/picard/MarkDuplicates.py
multiqc/modules/picard/MarkIlluminaAdapters.py
multiqc/modules/picard/OxoGMetrics.py
multiqc/modules/picard/QualityByCycleMetrics.py
multiqc/modules/picard/QualityScoreDistributionMetrics.py
multiqc/modules/picard/QualityYieldMetrics.py
multiqc/modules/picard/RnaSeqMetrics.py
multiqc/modules/picard/RrbsSummaryMetrics.py
multiqc/modules/picard/TargetedPcrMetrics.py
multiqc/modules/picard/ValidateSamFile.py
multiqc/modules/picard/VariantCallingMetrics.py
multiqc/modules/picard/WgsMetrics.py
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multiqc/modules/porechop/__init__.py
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multiqc/modules/qorts/__init__.py
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multiqc/modules/rockhopper/__init__.py
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multiqc/modules/rsem/__init__.py
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multiqc/modules/rseqc/__init__.py
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multiqc/modules/rseqc/gene_body_coverage.py
multiqc/modules/rseqc/infer_experiment.py
multiqc/modules/rseqc/inner_distance.py
multiqc/modules/rseqc/junction_annotation.py
multiqc/modules/rseqc/junction_saturation.py
multiqc/modules/rseqc/read_distribution.py
multiqc/modules/rseqc/read_duplication.py
multiqc/modules/rseqc/read_gc.py
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multiqc/templates/default/assets/js/toolbox.js
multiqc/templates/default/assets/js/packages/FileSaver.min.js
multiqc/templates/default/assets/js/packages/bootstrap.min.js
multiqc/templates/default/assets/js/packages/jquery-3.1.1.min.js
multiqc/templates/default/assets/js/packages/jquery-ui.min.js
multiqc/templates/default/assets/js/packages/jquery.tablesorter.min.js
multiqc/templates/default/assets/js/packages/jquery.toast.min.js
multiqc/templates/default/assets/js/packages/jszip.min.js
multiqc/templates/default/assets/js/packages/pako_inflate.min.js
multiqc/templates/default/assets/js/packages/plotly-2.27.0.js
multiqc/templates/default/assets/js/packages/plotly-2.27.0.min.js
multiqc/templates/default/assets/js/plots/bar.js
multiqc/templates/default/assets/js/plots/box.js
multiqc/templates/default/assets/js/plots/heatmap.js
multiqc/templates/default/assets/js/plots/line.js
multiqc/templates/default/assets/js/plots/scatter.js
multiqc/templates/default/assets/js/plots/violin.js
multiqc/templates/gathered/__init__.py
multiqc/templates/gathered/content.html
multiqc/templates/gathered/nav.html
multiqc/templates/geo/__init__.py
multiqc/templates/geo/includes.html
multiqc/templates/geo/assets/css/bootstrap.min.css
multiqc/templates/geo/assets/img/emailme.gif
multiqc/templates/geo/assets/img/flames.gif
multiqc/templates/geo/assets/img/glyphicons-halflings-white.png
multiqc/templates/geo/assets/img/glyphicons-halflings.png
multiqc/templates/geo/assets/img/hot.gif
multiqc/templates/geo/assets/img/mchammer.gif
multiqc/templates/geo/assets/img/microfab.gif
multiqc/templates/geo/assets/img/new.gif
multiqc/templates/geo/assets/img/new2.gif
multiqc/templates/geo/assets/img/progress.gif
multiqc/templates/geo/assets/img/rainbow.gif
multiqc/templates/geo/assets/img/stars.gif
multiqc/templates/sections/__init__.py
multiqc/templates/sections/content.html
multiqc/templates/simple/__init__.py
multiqc/templates/simple/foot.html
multiqc/templates/simple/footer.html
multiqc/templates/simple/header.html
multiqc/templates/simple/includes.html
multiqc/templates/simple/nav.html
multiqc/templates/simple/toolbox.html
multiqc/utils/__init__.py
multiqc/utils/config.py
multiqc/utils/megaqc.py
multiqc/utils/mqc_colour.py
multiqc/utils/pyaml_env.py
multiqc/utils/report.py
multiqc/utils/testing.py
multiqc/utils/util_functions.py
tests/test_cmdline.py
tests/test_custom_content.py
tests/test_interactive.py
tests/test_modules_run.py
tests/test_output_options.py
tests/test_plots.py
tests/test_sample_name_cleaning.py
tests/test_search_files.py
tests/test_software_versions.py