GDI_Addition_IDTK-Contentathon#383
Conversation
svarona
changed the title
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Some general points:
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Hi @bedroesb ! All your suggestions have been implemented. I hope everything is OK! |
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@jaimeozaez This is really great! I don't have the rights to edit this PR. 
Hence the workflow failing |
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@bedroesb fixed! It should now be working. |
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Same for |
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@bedroesb there is now the same error with amrfinderPlus. It would be great if the workflow would check all the tool names. |
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@jaimeozaez this is a hard error from Jekyll itself, using the exact same pipeline we use to deploy. I am afraid that catching the errors is difficult. Deploying the website yourself locally or on your fork is the easiest to know in advance if there will be errors. |
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@bedroesb this time seems that all worked well! :) |
| - **Reproducibility and Robustness**: Reproducibility and robustness of the biomolecular analysis methods used are crucial for ensuring the consistency and reliability of the results across different laboratories and researchers. Therefore, it is essential to evaluate the reproducibility and robustness of the methods used, including the variability of results obtained by different operators, equipment, and reagents. | ||
| - **Data Quality Assessment and Reporting**: Data quality assessment and reporting are critical for ensuring the accuracy and reliability of the results and communicating the findings to stakeholders effectively. This includes implementing appropriate data quality control measures, such as quality assessment metrics and statistical analysis, to identify and correct potential sources of error and ensure the accuracy and reliability of the data. Additionally, clear and concise reporting of the results, including appropriate data visualisation and interpretation, can help communicate the findings effectively to stakeholders. | ||
| - **Sequencing quality control**: Information and tools for the assessment of the quality of the sequencing data in the context of COVID-19 can be found in the publication by the COVID-19 Host Genetics Initiative (HGI) on the [Whole Exome/Genome Sequencing Analysis Plan](https://github.com/covid19-hg/covid19_sequencing?tab=readme-ov-file). | ||
| - **Benchmarking studies**: To obtain comparative quality assessment of the applied laboratory and analytical procedure, the participation in benchmarking studies is advised. Benchmarking studies can be performed in different ways, depending on the scientific discipline. The quality of sample processing results of aliquots from the same sample across several laboratories can be compared and reasons for quality deviations can possibly be identified. Benchmarking bioinformatics workflows can be done e.g. by providing mock genomes to the study participants and identifying those workflows that perform best in in silico identification or discovery of the respective trait in question (e.g. a variant, deletion of certain length, etc.). In the field of COVID-19, several benchmarking studies have been performed, e.g. for the sequencing of viral genomes (https://pubmed.ncbi.nlm.nih.gov/34308277/), or for benchmarking bioinformatics approaches for virus identification workflows (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03236-4; https://www.nature.com/articles/s41598-023-31368-3; https://www.biorxiv.org/content/10.1101/2023.08.07.552334v2.full; https://www.sciencedirect.com/science/article/pii/S138665322100175X). |
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Last comment, I promise! :) here these long urls look a bit off when rendered.
Could you replace them with the author + date, and the DOI behind them? See example below. @jaimeozaez
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I will also tag @svarona I think this is the only blocker anymore
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Don't forget to add you details to: https://github.com/BU-ISCIII/infectious-diseases-toolkit/blob/update_documentation/_data/CONTRIBUTORS.yaml So we can attribute accordingly. |
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@bedroesb I believe everything is ready! 😊 |
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Great! Lets merge! I will push a new item immediately after. |
3 participants
Update of the documentation following the contentathon. Updated files: