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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/reportho analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2024-07-18, 13:31 UTC based on data in: /fusion/s3/nf-core-awsmegatests/work/reportho/work-42b305199b903365b71e7a8554cfcc6a822da8a8/9f/d42634a1dcd5496fc94a36aa834586


        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        CONVERT_FASTABiopython1.83
        Python3.11.0
        CONVERT_PHYLIPBiopython1.83
        Python3.11.0
        FASTMEfastme2.1.6.1
        FETCH_AFDB_STRUCTURESPython3.11.0
        Python Requests2.31.0
        FETCH_INSPECTOR_GROUP_ONLINEOrthoInspector DatabaseEukaryota2023
        Python3.11.0
        Python Requests2.31.0
        FETCH_OMA_GROUP_ONLINEOMA API1.1
        OMA DatabaseAll.Jul2023
        Python3.11.0
        Python Requests2.31.0
        FETCH_PANTHER_GROUP_ONLINEPanther Databasenull
        Python3.11.0
        Python Requests2.31.0
        FETCH_SEQUENCES_ONLINEOMA API1.1
        OMA DatabaseAll.Jul2023
        Python3.11.0
        Python Requests2.31.0
        FILTER_FASTAPython3.11.0
        FILTER_HITSPython3.11.0
        IQTREEiqtree2.3.0
        MAKE_HITS_TABLEPython3.11.0
        MAKE_REPORTNode22.1.0
        React18.3.1
        Yarn1.22.19
        MAKE_SCORE_TABLEPython3.11.0
        MAKE_STATSPython3.11.0
        MERGE_CSVcsvtk0.30.0
        MERGE_HITScsvtk0.30.0
        MERGE_STATScsvtk0.30.0
        PLOT_FASTMEr-base4.3.3
        PLOT_IQTREEr-base4.3.3
        PLOT_ORTHOLOGSr-base4.3.3
        STATS2CSVPyYAML5.4.1
        Python3.9.6
        TCOFFEE_3DALIGNpigz2.8)
        tcoffee13.46.0.919e8c6b
        WRITE_SEQINFOPython3.11.0
        Python Requests2.31.0
        WorkflowNextflow23.10.1
        nf-core/reporthov1.0.1-g42b3051

        nf-core/reportho Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.

        Methods

        Data was processed using nf-core/reportho v1.0.1 (doi: 10.5281/zenodo.11574565) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v23.10.1 (Di Tommaso et al., 2017) with the following command:

        nextflow run 'https://github.com/nf-core/reportho' -name maniac_descartes -params-file 'https://api.cloud.seqera.io/ephemeral/Rv-kRNA4a0DIx2JlNYi5Bw.json' -with-tower -r 42b305199b903365b71e7a8554cfcc6a822da8a8 -profile test_full

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/reportho Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        revision
        1.0.1
        runName
        maniac_descartes
        launchDir
        /
        workDir
        /nf-core-awsmegatests/work/reportho/work-42b305199b903365b71e7a8554cfcc6a822da8a8
        projectDir
        /.nextflow/assets/nf-core/reportho
        userName
        root
        profile
        test_full
        configFiles
        N/A

        Input/output options

        input
        https://raw.githubusercontent.com/nf-core/test-datasets/reportho/testdata/samplesheet/samplesheet.csv
        outdir
        s3://nf-core-awsmegatests/reportho/results-42b305199b903365b71e7a8554cfcc6a822da8a8

        Ortholog search options

        eggnog_path
        http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/1/1_members.tsv.gz
        eggnog_idmap_path
        http://eggnog5.embl.de/download/eggnog_5.0/id_mappings/uniprot/latest.Eukaryota.tsv.gz
        min_score
        3

        Downstream analysis options

        use_structures
        true

        Institutional config options

        config_profile_name
        Full test profile
        config_profile_description
        Full test dataset to check pipeline function

        Generic options

        hook_url
        https://hooks.slack.com/services/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