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        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 1.27

        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/rnavar analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-05-06, 14:44 PDT based on data in: /gscratch/scrubbed/srlab/nxf.FHUE2SfYmw

        Software Versions

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

        GroupSoftwareVersion
        CAT_FASTQcat9.5
        ENSEMBLVEP_VEPensemblvep113.0
        tabix1.21
        FASTQCfastqc0.12.1
        GATK4_BEDTOINTERVALLISTgatk44.6.1.0
        GATK4_HAPLOTYPECALLERgatk44.6.1.0
        GATK4_INTERVALLISTTOOLSgatk44.6.1.0
        GATK4_MERGEVCFSgatk44.6.1.0
        GATK4_SPLITNCIGARREADSgatk44.6.1.0
        GATK4_VARIANTFILTRATIONgatk44.6.1.0
        PICARD_MARKDUPLICATESpicard3.3.0
        SAMTOOLS_FLAGSTATsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_MERGEsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        SNPEFF_SNPEFFsnpeff5.1d
        STAR_ALIGNgawk5.1.0
        samtools1.21
        star2.7.11b
        TABIXtabix1.2
        TABIX_BGZIPTABIXtabix1.2
        TABIX_TABIXtabix1.2
        WorkflowNextflow24.10.5
        nf-core/rnavarv1.1.0-g6a5ca78

        nf-core/rnavar Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnavar

        Methods

        Data was processed using nf-core/rnavar v1.1.0 (doi: 10.5281/zenodo.6669636) 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 v24.10.5 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/rnavar -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config -resume --input samplesheet.csv --fasta /gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.fasta --gtf /gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.genes-validated.gtf --tools merge --skip_baserecalibration true --outdir results

        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/rnavar Workflow Summary

        - this information is collected when the pipeline is started.URL: https://github.com/nf-core/rnavar

        Input/output options

        input
        samplesheet.csv
        outdir
        results
        tools
        merge

        Reference genome options

        fasta
        /gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.assembly.fasta
        genome
        GRCh38
        gtf
        /gscratch/srlab/strigg/GENOMES/Pocillopora_meandrina_HIv1.genes-validated.gtf
        snpeff_db
        GRCh38.105
        vep_cache_version
        110
        vep_genome
        GRCh38
        vep_species
        homo_sapiens

        Alignment options

        star_index
        s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/
        star_twopass
        true

        Pipeline stage options

        skip_baserecalibration
        true

        Institutional config options

        config_profile_contact
        Shelly A. Wanamaker @shellywanamaker
        config_profile_description
        UW Hyak Roberts labs cluster profile provided by nf-core/configs.
        config_profile_url
        https://faculty.washington.edu/sr320/

        Generic options

        trace_report_suffix
        2025-05-06_13-14-50

        Core Nextflow options

        configFiles
        /mmfs1/home/strigg/.nextflow/assets/nf-core/rnavar/nextflow.config, /gscratch/srlab/strigg/bin/uw_hyak_srlab.config
        containerEngine
        singularity
        launchDir
        /mmfs1/gscratch/scrubbed/strigg/analyses/20250506_rnavar
        profile
        standard
        projectDir
        /mmfs1/home/strigg/.nextflow/assets/nf-core/rnavar
        revision
        master
        runName
        focused_faggin
        userName
        strigg
        workDir
        /mmfs1/gscratch/scrubbed/strigg/analyses/20250506_rnavar/work

        MultiQC v1.27 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.