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jfy133 merged 26 commits into from
Jul 17, 2023
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Dynamic listing of citations/references of used tools in MultiQC methods section #308

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17d163a
Start adding dynamic citation insertion into methods description
jfy133 Jun 17, 2023
b4420eb
Add bibliography insert as well!
jfy133 Jun 17, 2023
d5b34f5
Update changelog
jfy133 Jun 17, 2023
4a0cae4
phrasing
jfy133 Jun 17, 2023
5c77e37
Apply suggestions from code review
jfy133 Jun 18, 2023
8359b06
Update methods_description_template.yml
jfy133 Jun 18, 2023
7742ab5
Update methods_description_template.yml
jfy133 Jun 18, 2023
b634084
Fix filtlong formating in citations
jfy133 Jun 25, 2023
462a752
Merge branch 'dev' into print-tool-citations
jfy133 Jul 7, 2023
7493860
Fix comma space dot issue
jfy133 Jul 12, 2023
eac28ba
Add check for database header to close #310
jfy133 Jun 29, 2023
5eef75d
Remove empty lines
jfy133 Jun 29, 2023
662b532
No need to check outdir for existence - Nextflow can create it on demand
robsyme Jul 7, 2023
f44f110
Add support for virus -e
jfy133 Jul 10, 2023
2e8a836
Update taxpasta version and add ganon support
jfy133 Jul 10, 2023
d72f2ba
Update CHANGELOG
jfy133 Jul 10, 2023
1b790e5
Merge branch 'dev' into print-tool-citations
jfy133 Jul 12, 2023
e5f7cce
Fix changelog
jfy133 Jul 12, 2023
dfff309
Start conmversoipn to lists
jfy133 Jul 12, 2023
d32774f
Add filtlong citation
jfy133 Jul 13, 2023
929fc4d
Switch to list based with better replaceAll
jfy133 Jul 13, 2023
bc5debb
Finalise text with DOI links!
jfy133 Jul 13, 2023
54b60ea
Merge branch 'dev' into print-tool-citations
jfy133 Jul 17, 2023
ee80255
Standardise and sync citation styles between citations.md and toolBib…
jfy133 Jul 17, 2023
4b5d82a
Update Mp3 to MP4 citation
jfy133 Jul 17, 2023
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And with citations
jfy133 Jul 17, 2023
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19 changes: 9 additions & 10 deletions CHANGELOG.md
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Expand Up @@ -7,16 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- New Classifers/Profilers
- [#298](https://github.com/nf-core/taxprofiler/pull/298) Added [ganon](https://pirovc.github.io/ganon/) (added by @jfy133)
- Additional functionality
- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing (added by @Midnighter)
- [#272](https://github.com/nf-core/taxprofiler/pull/272) Add saving of final 'analysis-ready-reads' to dedicated directory (❤️ to @alexhbnr for request, added by @jfy133)
- [#303](https://github.com/nf-core/taxprofiler/pull/303) Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
- [#315](https://github.com/nf-core/taxprofiler/pull/315) Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
- [#319](https://github.com/nf-core/taxprofiler/pull/319) Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
- [#323](https://github.com/nf-core/taxprofiler/pull/323) Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
- [#318](https://github.com/nf-core/taxprofiler/pull/318) Added the profiler MetaPhlAn4 and removed MetaPhlAn3 (added by @LilyAnderssonLee)
- [#298](https://github.com/nf-core/taxprofiler/pull/298) **New classifier** [ganon](https://pirovc.github.io/ganon/) (added by @jfy133)
- [#276](https://github.com/nf-core/taxprofiler/pull/276) Implemented batching in the KrakenUniq samples processing (added by @Midnighter)
- [#272](https://github.com/nf-core/taxprofiler/pull/272) Add saving of final 'analysis-ready-reads' to dedicated directory (❤️ to @alexhbnr for request, added by @jfy133)
- [#303](https://github.com/nf-core/taxprofiler/pull/303) Add support for taxpasta profile standardisation in single sample pipeline runs (❤️ to @artur-matysik for request, added by @jfy133)
- [#308](https://github.com/nf-core/taxprofiler/pull/308) Add citations and bibliographic information to the MultiQC methods text of tools used in a given pipeline run (added by @jfy133)
- [#315](https://github.com/nf-core/taxprofiler/pull/315) Updated to nf-core pipeline template v2.9 (added by @sofstam & @jfy133)
- [#319](https://github.com/nf-core/taxprofiler/pull/319) Added support for virus hit expansion in Kaiju (❤️ to @dnlrxn for requesting, added by @jfy133)
- [#323](https://github.com/nf-core/taxprofiler/pull/323) Add ability to skip sequencing quality control tools (❤️ to @vinisalazar for requesting, added by @jfy133)
- [#318](https://github.com/nf-core/taxprofiler/pull/318) Added the profiler MetaPhlAn4 and removed MetaPhlAn3 (added by @LilyAnderssonLee)

### `Fixed`

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48 changes: 29 additions & 19 deletions CITATIONS.md
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- [falco](https://doi.org/10.12688/f1000research.21142.2)

> de Sena Brandine G and Smith AD. Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research 2021, 8:1874
> de Sena Brandine, G., & Smith, A. D. (2021). Falco: high-speed FastQC emulation for quality control of sequencing data. F1000Research, 8(1874), 1874. https://doi.org/10.12688/f1000research.21142.2

- [fastp](https://doi.org/10.1093/bioinformatics/bty560)

> Chen, Shifu, Yanqing Zhou, Yaru Chen, and Jia Gu. 2018. Fastp: An Ultra-Fast All-in-One FASTQ Preprocessor. Bioinformatics 34 (17): i884-90. 10.1093/bioinformatics/bty560.
> Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics , 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560

- [AdapterRemoval2](https://doi.org/10.1186/s13104-016-1900-2)

> Schubert, Mikkel, Stinus Lindgreen, and Ludovic Orlando. 2016. AdapterRemoval v2: Rapid Adapter Trimming, Identification, and Read Merging. BMC Research Notes 9 (February): 88. doi:10.1186/s13104-016-1900-2.
> Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. https://doi.org/10.1186/s13104-016-1900-2

- [Porechop](https://github.com/rrwick/Porechop)

- [FILTLONG](https://github.com/rrwick/Filtlong)
> Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017). Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomics, 3(10), e000132. https://doi.org/10.1099/mgen.0.000132

- [Filtlong](https://github.com/rrwick/Filtlong)

> Wick R (2021) Filtlong, URL: https://github.com/rrwick/Filtlong

- [BBTools](http://sourceforge.net/projects/bbmap/)

> Bushnell B. (2022) BBMap, URL: http://sourceforge.net/projects/bbmap/

- [PRINSEQ++](https://doi.org/10.7287/peerj.preprints.27553v1)

> Cantu, Vito Adrian, Jeffrey Sadural, and Robert Edwards. 2019. PRINSEQ++, a Multi-Threaded Tool for Fast and Efficient Quality Control and Preprocessing of Sequencing Datasets. e27553v1. PeerJ Preprints. doi: 10.7287/peerj.preprints.27553v1.
> Cantu, V. A., Sadural, J., & Edwards, R. (2019). PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets (e27553v1). PeerJ Preprints. https://doi.org/10.7287/peerj.preprints.27553v1

- [Bowtie2](https://doi.org/10.1038/nmeth.1923)

> Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–359. doi: 10.1038/nmeth.1923
> Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4), 357–359. https://doi.org/10.1038/nmeth.1923

- [minimap2](https://doi.org/10.1093/bioinformatics/bty191)

> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics , 34(18), 3094–3100. doi: 10.1093/bioinformatics/bty191
> Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics , 34(18), 3094–3100. https://doi.org/10.1093/bioinformatics/bty191

- [SAMTools](https://doi.org/10.1093/gigascience/giab008)

> Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2). doi: 10.1093/gigascience/giab008
> Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2). https://doi.org/10.1093/gigascience/giab008

- [Bracken](https://doi.org/10.7717/peerj-cs.104)

> Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: Estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. doi: 10.7717/peerj-cs.104
> Lu, J., Breitwieser, F. P., Thielen, P., & Salzberg, S. L. (2017). Bracken: estimating species abundance in metagenomics data. PeerJ. Computer Science, 3(e104), e104. https://doi.org/10.7717/peerj-cs.104

- [Kraken2](https://doi.org/10.1186/s13059-019-1891-0)

> Wood, Derrick E., Jennifer Lu, and Ben Langmead. 2019. Improved Metagenomic Analysis with Kraken 2. Genome Biology 20 (1): 257. doi: 10.1186/s13059-019-1891-0.
> Wood, D. E., Lu, J., & Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biology, 20(1), 257. https://doi.org/10.1186/s13059-019-1891-0

- [KrakenUniq](https://doi.org/10.1186/s13059-018-1568-0)

> Breitwieser, Florian P., Daniel N. Baker, and Steven L. Salzberg. 2018. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology 19 (1): 198. doi: 10.1186/s13059-018-1568-0
> Breitwieser, F. P., Baker, D. N., & Salzberg, S. L. (2018). KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biology, 19(1), 198. https://doi.org/10.1186/s13059-018-1568-0

- [MetaPhlAn](https://doi.org/10.1038/s41587-023-01688-w)

> Blanco-Míguez, A., Beghini, F., Cumbo, F. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol (2023). doi: 10.1038/s41587-023-01688-w
> Blanco-Míguez, A., Beghini, F., Cumbo, F., McIver, L. J., Thompson, K. N., Zolfo, M., Manghi, P., Dubois, L., Huang, K. D., Thomas, A. M., Nickols, W. A., Piccinno, G., Piperni, E., Punčochář, M., Valles-Colomer, M., Tett, A., Giordano, F., Davies, R., Wolf, J., … Segata, N. (2023). Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nature Biotechnology, 1–12. https://doi.org/10.1038/s41587-023-01688-w

- [MALT](https://doi.org/10.1038/s41559-017-0446-6)

> Vågene, Åshild J., Alexander Herbig, Michael G. Campana, Nelly M. Robles García, Christina Warinner, Susanna Sabin, Maria A. Spyrou, et al. 2018. Salmonella Enterica Genomes from Victims of a Major Sixteenth-Century Epidemic in Mexico. Nature Ecology & Evolution 2 (3): 520-28. doi: 10.1038/s41559-017-0446-6.
> Vågene, Å. J., Herbig, A., Campana, M. G., Robles García, N. M., Warinner, C., Sabin, S., Spyrou, M. A., Andrades Valtueña, A., Huson, D., Tuross, N., Bos, K. I., & Krause, J. (2018). Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution, 2(3), 520–528. https://doi.org/10.1038/s41559-017-0446-6

- [MEGAN](https://doi.org/10.1371/journal.pcbi.1004957)

> Huson, Daniel H., Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, and Rewati Tappu. 2016. “MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.” PLoS Computational Biology 12 (6): e1004957. doi: 10.1371/journal.pcbi.1004957.
> Huson, D. H., Beier, S., Flade, I., Górska, A., El-Hadidi, M., Mitra, S., Ruscheweyh, H.-J., & Tappu, R. (2016). MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Computational Biology, 12(6), e1004957. https://doi.org/10.1371/journal.pcbi.1004957

- [DIAMOND](https://doi.org/10.1038/nmeth.3176)

> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.
> Buchfink, B., Xie, C., & Huson, D. H. (2015). Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1), 59–60. https://doi.org/10.1038/nmeth.3176

- [Centrifuge](https://doi.org/10.1101/gr.210641.116)

> Kim, Daehwan, Li Song, Florian P. Breitwieser, and Steven L. Salzberg. 2016. “Centrifuge: Rapid and Sensitive Classification of Metagenomic Sequences.” Genome Research 26 (12): 1721-29. doi: 10.1101/gr.210641.116.
> Kim, D., Song, L., Breitwieser, F. P., & Salzberg, S. L. (2016). Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Research, 26(12), 1721–1729. https://doi.org/10.1101/gr.210641.116

- [Kaiju](https://doi.org/10.1038/ncomms11257)

> Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257. doi: 10.1038/ncomms11257
> Menzel, P., Ng, K. L., & Krogh, A. (2016). Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nature Communications, 7, 11257. https://doi.org/10.1038/ncomms11257

- [mOTUs](https://doi.org/10.1186/s40168-022-01410-z)

> Ruscheweyh, H.-J., Milanese, A., Paoli, L., Karcher, N., Clayssen, Q., Keller, M. I., Wirbel, J., Bork, P., Mende, D. R., Zeller, G., & Sunagawa, S. (2022). Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome, 10(1), 212. doi: 10.1186/s40168-022-01410-z
> Ruscheweyh, H.-J., Milanese, A., Paoli, L., Karcher, N., Clayssen, Q., Keller, M. I., Wirbel, J., Bork, P., Mende, D. R., Zeller, G., & Sunagawa, S. (2022). Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. Microbiome, 10(1), 212. https://doi.org/10.1186/s40168-022-01410-z

- [ganon](https://doi.org/10.1093/bioinformatics/btaa458)

> Piro, V. C., Dadi, T. H., Seiler, E., Reinert, K., & Renard, B. Y. (2020). Ganon: Precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics (Oxford, England), 36(Suppl_1), i12–i20. doi: 10.1093/bioinformatics/btaa458
> Piro, V. C., Dadi, T. H., Seiler, E., Reinert, K., & Renard, B. Y. (2020). Ganon: Precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics (Oxford, England), 36(Suppl_1), i12–i20. https://doi.org/10.1093/bioinformatics/btaa458

- [Krona](https://doi.org/10.1186/1471-2105-12-385)

> Ondov, Brian D., Nicholas H. Bergman, and Adam M. Phillippy. 2011. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics 12 (1): 385. doi: 10.1186/1471-2105-12-385.

- [TAXPASTA](https://doi.org/10.21105/joss.05627)

> Beber, M. E., Borry, M., Stamouli, S., & Fellows Yates, J. A. (2023). TAXPASTA: TAXonomic Profile Aggregation and STAndardisation. Journal of Open Source Software, 8(87), 5627. https://doi.org/10.21105/joss.05627

## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)
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