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| Original file line number | Diff line number | Diff line change |
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| id: "avantonder-bacQC-methods-description" | ||
| description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." | ||
| section_name: "avantonder/bacQC Methods Description" | ||
| section_href: "https://github.com/avantonder/bacQC" | ||
| plot_type: "html" | ||
| data: | | ||
| <h4>Methods</h4> | ||
| <p>Data was processed using avantonder/bacQC v${workflow.manifest.version} ${doi_text} utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p> | ||
| <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p> | ||
| <pre><code>${workflow.commandLine}</code></pre> | ||
| <p>${tool_citations}</p> | ||
| <h4>References</h4> | ||
| <ul> | ||
| <li>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: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li> | ||
| <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The avantonder framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li> | ||
| <li>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: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li> | ||
| <li>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: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li> | ||
| ${tool_bibliography} | ||
| </ul> | ||
| <div class="alert alert-info"> | ||
| <h5>Notes:</h5> | ||
| <ul> | ||
| ${nodoi_text} | ||
| <li>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!</li> | ||
| <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li> | ||
| </ul> | ||
| </div> |
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| report_comment: > | ||
| This report has been generated by the <a href="https://github.com/avantonder/bacQC" target="_blank">bacQC</a> | ||
| analysis pipeline. For information about how to interpret these results, please see the | ||
| <a href="https://github.com/avantonder/bacQC" target="_blank">documentation</a>. | ||
| <a href="https://github.com/avantonder/bacQC/blob/main/docs/output.md" target="_blank">documentation</a>. | ||
| data_format: "yaml" | ||
| max_table_rows: 10000 | ||
| report_section_order: | ||
| "avantonder-bacQC-methods-description": | ||
| order: -1000 | ||
| software_versions: | ||
| order: -1001 | ||
| "avantonder-bacqc-summary": | ||
| order: -1002 | ||
| general_stats": | ||
| order: 1000 | ||
| fastqc: | ||
| order: 900 | ||
| fastp: | ||
| order: 800 | ||
| kraken: | ||
| order: 700 | ||
| bracken: | ||
| order: 600 | ||
|
|
||
| export_plots: true | ||
|
|
||
| run_modules: | ||
| - custom_content | ||
| - fastqc | ||
| - fastp | ||
| - kraken | ||
| - custom_content | ||
|
|
||
| module_order: | ||
| - fastqc: | ||
| name: "PREPROCESS: FastQC (raw reads)" | ||
| top_modules: | ||
| - "fastqc": | ||
| name: "FastQC (raw reads)" | ||
| info: "This section of the report shows FastQC results for the raw reads before adapter trimming." | ||
| path_filters: | ||
| - "./fastqc/*.zip" | ||
| - fastp: | ||
| name: "PREPROCESS: fastp (adapter trimming)" | ||
| - "*_fastqc.zip" | ||
| - "fastp": | ||
| name: "fastp (adapter trimming)" | ||
| info: "This section of the report shows fastp results for reads after adapter and quality trimming." | ||
| - kraken: | ||
| name: "PREPROCESS: Kraken 2" | ||
| info: "This section of the report shows Kraken 2 classification results for reads after adapter trimming with fastp." | ||
| - "kraken": | ||
| name: "Kraken" | ||
| path_filters: | ||
| - "*.kraken2.report.txt" | ||
| - "kraken": | ||
| name: "Bracken" | ||
| anchor: "bracken" | ||
| target: "Bracken" | ||
| doi: "10.7717/peerj-cs.104" | ||
| info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree." | ||
| path_filters: | ||
| - "*.kraken2.report_bracken.txt" | ||
|
|
||
| report_section_order: | ||
| summary_assembly_metrics: | ||
| before: summary_variants_metrics | ||
| software_versions: | ||
| order: -1001 | ||
| "nf-core-bacqc-summary": | ||
| order: -1002 | ||
| table_columns_placement: | ||
| FastQC (raw reads): | ||
| total_sequences: 100 | ||
| avg_sequence_length: 110 | ||
| median_sequence_length: 120 | ||
| percent_duplicates: 130 | ||
| percent_gc: 140 | ||
| percent_fails: 150 | ||
| fastp (adapter trimming): | ||
| pct_adapter: 300 | ||
| pct_surviving: 310 | ||
| pct_duplication: 320 | ||
| after_filtering_gc_content: 330 | ||
| after_filtering_q30_rate: 340 | ||
| after_filtering_q30_bases: 350 | ||
| filtering_result_passed_filter_reads: 360 | ||
| Bracken: | ||
| "% Unclassified": 1200 | ||
| "% Top 5": 1210 | ||
| Kraken: | ||
| "% Unclassified": 1600 | ||
| "% Top 5": 1610 | ||
|
|
||
| table_columns_visible: | ||
| FastQC (raw reads): | ||
| total_sequences: True | ||
| avg_sequence_length: True | ||
| percent_duplicates: True | ||
| percent_gc: True | ||
| percent_fails: False | ||
| Kraken: False | ||
| Bracken: False | ||
|
|
||
| table_columns_name: | ||
| FastQC (raw reads): | ||
| total_sequences: "Nr. Input Reads" | ||
| avg_sequence_length: "Length Input Reads" | ||
| percent_gc: "% GC Input Reads" | ||
| percent_duplicates: "% Dups Input Reads" | ||
| percent_fails: "% Failed Input Reads" | ||
|
|
||
| export_plots: true | ||
| section_comments: | ||
| general_stats: "By default, all read count columns are displayed as millions (M) of reads." |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/nf-core/denovotranscript/master/assets/schema_input.json", | ||
| "title": "nf-core/denovotranscript pipeline - params.input schema", | ||
| "description": "Schema for the file provided with params.input", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "sample": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Sample name must be provided and cannot contain spaces", | ||
| "meta": ["id"] | ||
| }, | ||
| "fastq_1": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "exists": true, | ||
| "pattern": "^\\S+\\.f(ast)?q\\.gz$", | ||
| "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" | ||
| }, | ||
| "fastq_2": { | ||
| "type": "string", | ||
| "format": "file-path", | ||
| "exists": true, | ||
| "pattern": "^\\S+\\.f(ast)?q\\.gz$", | ||
| "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" | ||
| } | ||
| }, | ||
| "required": ["sample", "fastq_1"] | ||
| } | ||
| } |
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