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Nextflow

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Nextflow
Original author(s)Paolo Di Tommaso
Developer(s)Seqera Labs, Centre for Genomic Regulation
Initial releaseApril 9, 2013; 11 years ago (2013-04-09)
Stable release
v23.10.1 / January 12, 2024; 9 months ago (2024-01-12)
Preview release
v24.02.0-edge / March 9, 2024; 7 months ago (2024-03-09)
Repositoryhttps://github.com/nextflow-io/nextflow
Written inGroovy, Java
Operating systemLinux, macOS, WSL
TypeScientific workflow system, Dataflow programming, Big data
LicenseApache License 2.0
Websitenextflow.io

Nextflow is a scientific workflow system predominantly used for bioinformatic data analysis. It establishes standards for programmatically creating a series of dependent computational steps and facilitates their execution on various local and cloud resources.[1][2]

Purpose

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Many scientific data analyses require a significant amount of sequential processing steps. Custom scripts may suffice when developing new methods or infrequently running particular analyses, but scale poorly to complex task successions or many samples.[3][4][5]

Scientific workflow systems like Nextflow allow formalizing an analysis as a data analysis pipeline. Pipelines, also known as workflows, the specify order and conditions of computing steps. They are accomplished by special purpose programs, so-called workflow executors, which ensure predictable and reproducible behavior in various computing environments.[3][6][7][8]

Workflow systems also provide built-in solutions to common challenges of workflow development, such as the application to multiple samples, the validation of input and intermediate results, conditional execution of steps, error handling, and report generation. Advanced features of workflow systems may also include scheduling capabilities, graphical user interfaces for monitoring workflow executions, and the management of dependencies by containerizing the whole workflow or its components.[9][10]

Typically, scientific workflow systems initially present a steep learning challenge as all their features and complexities are built on in addition to the actual analysis. However, the standards and abstraction imposed by workflow systems ultimately improve the traceability of analysis steps, which is particularly relevant when collaborating on pipeline development, as is customary in scientific settings.[11]

Characteristics

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Specification of workflows

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In Nextflow, pipelines are constructed from individual processes that work in parallel to perform computational tasks. Each process is defined with input requirements and output declarations. Instead of running in a fixed sequence, a process starts executing when all its input requirements are fulfilled. By specifying the output of one process as the input of another, a logical and sequential connection between processes is established.[12]

This reactive implementation is a key design pattern of Nextflow and is also known as the functional dataflow model.[13]

Processes and entire workflows are programmed in a domain-specific language (DSL) which is provided by Nextflow which is based on Apache Groovy.[14] While Nextflow's DSL is used to declare the workflow logic, developers can use their scripting language of choice within a process and mix multiple languages in a workflow. It is also possible to port existing scripts and workflows to Nextflow. Supported scripting languages include bash, csh, ksh, Python, Ruby, and R. Any scripting language that uses the standard Unix shebang declaration (#!/bin/bash) is compatible with Nextflow.

Below is an example of a workflow consisting of only one process:

process hello_world {
    input:
    val greeting

    output:
    path "${greeting}.txt"

    script:
    """
    echo "${greeting} World!" > ${greeting}.txt
    """
}

workflow {
    Channel.of("Hello", "Ciao", "Hola", "Bonjour") | hello_world
}

To enable easy collaboration on workflows, Nextflow natively support for source-code management systems and DevOps platforms including GitHub, GitLab, and others.[15]

Execution of workflows

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Nextflow's DSL allows you to deploy and run workflows across different computing environments without having to modify the pipeline code. Nextflow comes with specific executors for various platforms, including major cloud providers. It supports the following environments for pipeline execution:[16]

  • Local: This is the default executor where Nextflow pipelines run on Linux or Mac OS, and the execution occurs on the computer where the pipeline is launched.
  • HPC workload managers: Nextflow supports workload managers such as Slurm, SGE, LSF, Moab, PBS Pro, PBS/Torque, HTCondor, NQSII, and OAR.
  • Kubernetes: Nextflow can be used with local or cloud-based Kubernetes implementations (GKE, EKS, or AKS).
  • Cloud batch services: It is compatible with AWS Batch[17] and Azure Batch[18]
  • Other environments: Nextflow can also be used with Apache Ignite, Google Life Sciences, and various container frameworks for portability.[19]

Containers for portability across computing environments

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In Nextflow, there is tight integration with software containers. Workflows and single processes can utilize containers for their execution across different computing environments, eliminating the need for complex installation and configuration routines.[3][20]

Nextflow supports container frameworks such as Docker, Singularity, Charliecloud, Podman, and Shifter. These containers can be automatically retrieved from external repositories when the pipeline is executed. Additionally, it was revealed at Nextflow Summit 2022 that future versions of Nextflow will support a dedicated container provisioning service for better integration of customized containers into workflows.[21][22]

Developmental history

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Nextflow was originally developed at the Centre for Genomic Regulation in Spain and released as an open-source project on GitHub in July 2013.[23] In October 2018, the project license for Nextflow was changed from GPLv3 to Apache 2.0.[24]

In July 2018, Seqera Labs was launched as a spin-off from the Centre for Genomic Regulation.[20] The company employs many of Nextflow's core developers and maintainers and provides commercial services and consulting with a focus on Nextflow. [25]

In July 2020, a major extension and revision of Nextflow's domain-specific language was introduced to allow for sub-workflows and additional improvements.[26] In the same year, monthly downloads of Nextflow reached approximately 55,000.[20]

Adoption and reception

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The nf-core community

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The nf-core project has been adopted by several sequencing facilities including the Centre for Genomic Regulation,[27] the Quantitative Biology Center in Tübingen, the Francis Crick Institute, A*STAR Genome Institute of Singapore, and the Swedish National Genomics Infrastructure as their preferred Scientific workflow system, .[20] These facilities have collaborated to share, harmonize, and curate bioinformatic pipelines,[28][29][30][31] leading to the creation of the nf-core project.[32] Led by Phil Ewels from the Swedish National Genomics Infrastructure,[33][34] nf-core focuses on ensuring reproducibility and portability of pipelines across different hardware, operating systems, and software versions. In July 2020, Nextflow and nf-core received a grant from the Chan Zuckerberg Initiative in recognition of their importance as open-source software.[35] As of 2022, the nf-core organization hosts 73 Nextflow pipelines for the biosciences and more than 700 process modules. With more than 500 developers and scientists involved, it is the largest collaborative effort and community for developing bioinformatic data analysis pipelines.[36]

By domain and research subject

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Nextflow is the preferred tool for processing sequencing data and conducting genomic data analysis by domain and research subject. Over the past five years, numerous pipelines have been published for various applications and analyses in the genomics field.

One notable use case is its role in pathogen surveillance during the COVID-19 pandemic.[37] Swift and highly automated processing of raw data, variant analysis, and lineage designation were essential for monitoring the emergence of new virus variants and tracing their global spread. Nextflow-enabled pipelines played a crucial role in this effort.[38] [39] [40] [41] [42] [43] [44]

Nextflow also plays a significant role for the non-profit plasmid repository Addgene, using it to confirm the integrity of all deposited plasmids.[45]

In addition to genomics, Nextflow is gaining popularity in other domains of biomedical data processing, where complex workflows on large amounts of primary data are required. These domains include Drug screening,[46] Diffusion magnetic resonance imaging (dMRI) in radiology,[47] and mass spectrometry data processing,[48][49][50] the latter with a particular focus on proteomics[51] [52] [53] [54] [55] [56] [57] [58]

References

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  1. ^ Strozzi, Francesco; Janssen, Roel; Wurmus, Ricardo; Crusoe, Michael R.; Githinji, George; Di Tommaso, Paolo; Belhachemi, Dominique; Möller, Steffen; Smant, Geert; De Ligt, Joep; Prins, Pjotr (2019). "Scalable Workflows and Reproducible Data Analysis for Genomics". Evolutionary Genomics. Methods in Molecular Biology. Vol. 1910. pp. 723–745. doi:10.1007/978-1-4939-9074-0_24. ISBN 978-1-4939-9073-3. PMC 7613310. PMID 31278683.
  2. ^ Gao, Mingxuan; Ling, Mingyi; Tang, Xinwei; Wang, Shun; Xiao, Xu; Qiao, Ying; Yang, Wenxian; Yu, Rongshan (2021). "Comparison of high-throughput single-cell RNA sequencing data processing pipelines". Briefings in Bioinformatics. 22 (3). doi:10.1093/bib/bbaa116. PMID 34020539.
  3. ^ a b c Wratten, Laura; Wilm, Andreas; Göke, Jonathan (October 2021). "Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers". Nature Methods. 18 (10): 1161–1168. doi:10.1038/s41592-021-01254-9. PMID 34556866. S2CID 237616424.
  4. ^ Terrón-Camero, Laura C.; Gordillo-González, Fernando; Salas-Espejo, Eduardo; Andrés-León, Eduardo (2022). "Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice". Genes. 13 (12): 2280. doi:10.3390/genes13122280. PMC 9777648. PMID 36553546.
  5. ^ Federico, Anthony; Karagiannis, Tanya; Karri, Kritika; Kishore, Dileep; Koga, Yusuke; Campbell, Joshua D.; Monti, Stefano (2019). "Pipeliner: A Nextflow-Based Framework for the Definition of Sequencing Data Processing Pipelines". Frontiers in Genetics. 10: 614. doi:10.3389/fgene.2019.00614. PMC 6609566. PMID 31316552.
  6. ^ Kolpakov, Fedor; Akberdin, Ilya; Kiselev, Ilya; Kolmykov, Semyon; Kondrakhin, Yury; Kulyashov, Mikhail; Kutumova, Elena; Pintus, Sergey; Ryabova, Anna; Sharipov, Ruslan; Yevshin, Ivan; Zhatchenko, Sergey; Kel, Alexander (2022). "BioUML—towards a universal research platform". Nucleic Acids Research. 50 (W1): W124–W131. doi:10.1093/nar/gkac286. PMC 9252820. PMID 35536253.
  7. ^ Yukselen, Onur; Turkyilmaz, Osman; Ozturk, Ahmet Rasit; Garber, Manuel; Kucukural, Alper (2020). "Dolphin Next: A distributed data processing platform for high throughput genomics". BMC Genomics. 21 (1): 310. doi:10.1186/s12864-020-6714-x. PMC 7168977. PMID 32306927.
  8. ^ Yuen, Denis; Cabansay, Louise; Duncan, Andrew; Luu, Gary; Hogue, Gregory; Overbeck, Charles; Perez, Natalie; Shands, Walt; Steinberg, David; Reid, Chaz; Olunwa, Nneka; Hansen, Richard; Sheets, Elizabeth; o'Farrell, Ash; Cullion, Kim; o'Connor, Brian D; Paten, Benedict; Stein, Lincoln (2021). "The Dockstore: Enhancing a community platform for sharing reproducible and accessible computational protocols". Nucleic Acids Research. 49 (W1): W624–W632. doi:10.1093/nar/gkab346. PMC 8218198. PMID 33978761.
  9. ^ Ahmed, Azza E.; Allen, Joshua M.; Bhat, Tajesvi; Burra, Prakruthi; Fliege, Christina E.; Hart, Steven N.; Heldenbrand, Jacob R.; Hudson, Matthew E.; Istanto, Dave Deandre; Kalmbach, Michael T.; Kapraun, Gregory D.; Kendig, Katherine I.; Kendzior, Matthew Charles; Klee, Eric W.; Mattson, Nate; Ross, Christian A.; Sharif, Sami M.; Venkatakrishnan, Ramshankar; Fadlelmola, Faisal M.; Mainzer, Liudmila S. (2021). "Design considerations for workflow management systems use in production genomics research and the clinic". Scientific Reports. 11 (1): 21680. Bibcode:2021NatSR..1121680A. doi:10.1038/s41598-021-99288-8. PMC 8569008. PMID 34737383.
  10. ^ Baichoo, Shakuntala; Souilmi, Yassine; Panji, Sumir; Botha, Gerrit; Meintjes, Ayton; Hazelhurst, Scott; Bendou, Hocine; Beste, Eugene de; Mpangase, Phelelani T.; Souiai, Oussema; Alghali, Mustafa; Yi, Long; o'Connor, Brian D.; Crusoe, Michael; Armstrong, Don; Aron, Shaun; Joubert, Fourie; Ahmed, Azza E.; Mbiyavanga, Mamana; Heusden, Peter van; Magosi, Lerato E.; Zermeno, Jennie; Mainzer, Liudmila Sergeevna; Fadlelmola, Faisal M.; Jongeneel, C. Victor; Mulder, Nicola (2018). "Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics". BMC Bioinformatics. 19 (1): 457. doi:10.1186/s12859-018-2446-1. PMC 6264621. PMID 30486782.
  11. ^ Jackson, Michael; Kavoussanakis, Kostas; Wallace, Edward W. J. (2021). "Using prototyping to choose a bioinformatics workflow management system". PLOS Computational Biology. 17 (2): e1008622. Bibcode:2021PLSCB..17E8622J. doi:10.1371/journal.pcbi.1008622. PMC 7906312. PMID 33630841.
  12. ^ Tommaso, Paolo Di; Floden, Evan W.; Magis, Cedrik; Palumbo, Emilio; Notredame, Cedric (2017). "Nextflow : Un outil efficace pour l'amélioration de la stabilité numérique des calculs en analyse génomique". Biologie Aujourd'hui. 211 (3): 233–237. doi:10.1051/jbio/2017029. PMID 29412134.
  13. ^ "Nextflow Documentation - Channels". docs.nextflow.io. Retrieved 6 June 2022.
  14. ^ "Nextflow Documentation - Domain Specific Language (DSL) 2". docs.nextflow.io. Retrieved 6 June 2022.
  15. ^ "Nextflow Documentation - Pipeline Sharing". docs.nextflow.io. Retrieved 6 June 2022.
  16. ^ "Nextflow Documentation - Executors". docs.nextflow.io. Retrieved 6 June 2022.
  17. ^ "Nextflow Documentation - Amazon Cloud". docs.nextflow.io. Retrieved 6 June 2022.
  18. ^ "Nextflow Documentation - Azure Cloud". docs.nextflow.io. Retrieved 6 June 2022.
  19. ^ "Nextflow Documentation - Google Cloud". docs.nextflow.io. Retrieved 6 June 2022.
  20. ^ a b c d Di Tomasso, Paolo (14 October 2021). "The story of Nextflow: Building a modern pipeline orchestrator". eLifeSciences.org. Retrieved 6 June 2022.
  21. ^ "Nextflow Documentation - Containers". docs.nextflow.io. Retrieved 7 June 2022.
  22. ^ Di Tommaso, Paolo (13 October 2022). "Nextflow and the future of containers". YouTube. Retrieved 17 November 2022.
  23. ^ "Release Version 0.3.0 · nextflow-io/nextflow". GitHub. Retrieved 31 May 2022.
  24. ^ Di Tomasso, Paolo (24 October 2018). "Goodbye zero, Hello Apache!". Nextflow.io/blog. Retrieved 7 June 2022.
  25. ^ Di Tommaso, Paolo (8 October 2019). "Introducing Nextflow Tower - Seamless monitoring of data analysis workflows from anywhere". Seqera.IO. Retrieved 7 June 2022.
  26. ^ Di Tommaso, Paolo (24 July 2020). "Nextflow DSL 2 is here!". Nextflow.IO/blog. Retrieved 7 June 2022.
  27. ^ Di Tomasso, Paolo; Chatzou, Maria; Floden, Evan; Prieto Barja, Pablo; Palumbo, Emilio; Notredame, Cedric (11 April 2017). "Nextflow enables reproducible computational workflows". Nature Biotechnology. 35 (4): 316–319. doi:10.1038/nbt.3820. PMID 28398311. S2CID 9690740. Retrieved 7 June 2022.
  28. ^ Fellows Yates, James A.; Lamnidis, Thiseas C.; Borry, Maxime; Andrades Valtueña, Aida; Fagernäs, Zandra; Clayton, Stephen; Garcia, Maxime U.; Neukamm, Judith; Peltzer, Alexander (2021). "Reproducible, portable, and efficient ancient genome reconstruction with nf-core/Eager". PeerJ. 9: e10947. doi:10.7717/peerj.10947. PMC 7977378. PMID 33777521.
  29. ^ Krakau, Sabrina; Straub, Daniel; Gourlé, Hadrien; Gabernet, Gisela; Nahnsen, Sven (2022). "Nf-core/Mag: A best-practice pipeline for metagenome hybrid assembly and binning". Nar Genomics and Bioinformatics. 4: lqac007. doi:10.1093/nargab/lqac007. PMC 8808542. PMID 35118380.
  30. ^ Garcia, Maxime; Juhos, Szilveszter; Larsson, Malin; Olason, Pall I.; Martin, Marcel; Eisfeldt, Jesper; Dilorenzo, Sebastian; Sandgren, Johanna; Díaz De Ståhl, Teresita; Ewels, Philip; Wirta, Valtteri; Nistér, Monica; Käller, Max; Nystedt, Björn (2020). "Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants". F1000Research. 9: 63. doi:10.12688/f1000research.16665.2. PMC 7111497. PMID 32269765.
  31. ^ Digby, Barry; Finn, Stephen P.; ó Broin, Pilib (2023). "Nf-core/Circrna: A portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs". BMC Bioinformatics. 24 (1): 27. doi:10.1186/s12859-022-05125-8. PMC 9875403. PMID 36694127.
  32. ^ Ewels, Philip; Peltzer, Alexander; Fillinger, Sven; Alneberg, Johannes; Patel, Harshil; Wilm, Andreas; Garcia, Maxime Ulysse; Di Tommaso, Paolo; Nahnsen, Sven (April 1, 2019). "Nf-core: Community curated bioinformatics pipelines". Research Gate. Retrieved June 30, 2022.
  33. ^ Zapata Garin, Claire-Alix. "nf-core: a community-driven initiative to standardise Nextflow-based pipelines". Lifebit.ai. Retrieved June 30, 2022.
  34. ^ "The nf-core community provides computational pipelines". SciLifeLab. February 14, 2020. Retrieved June 30, 2022.
  35. ^ "Nextflow and nf-core: Reproducible Workflows for the Scientific Community". Chan Zuckerberg Initiative. 27 July 2020. Retrieved 15 June 2022.
  36. ^ "nf-core Github organization". GitHub. Retrieved 18 November 2022.
  37. ^ Floden, Evan (5 November 2021). "Genetic Sequencing Will Enable Us To Win The Global Battle Against COVID-19".
  38. ^ Afolayan, Ayorinde O.; et al. (2021). "Overcoming Data Bottlenecks in Genomic Pathogen Surveillance". Clinical Infectious Diseases. 73 (Suppl_4): S267–S274. doi:10.1093/cid/ciab785. PMC 8634317. PMID 34850839.
  39. ^ Tilloy, Valentin; Cuzin, Pierre; Leroi, Laura; Guérin, Emilie; Durand, Patrick; Alain, Sophie (2022). "ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants". PLOS ONE. 17 (1): e0262953. Bibcode:2022PLoSO..1762953T. doi:10.1371/journal.pone.0262953. PMC 8791494. PMID 35081137.
  40. ^ Petit, Robert A.; Read, Timothy D. (2020). "Bactopia: A Flexible Pipeline for Complete Analysis of Bacterial Genomes". mSystems. 5 (4). doi:10.1128/mSystems.00190-20. PMC 7406220. PMID 32753501.
  41. ^ Pandolfo, Mattia; Telatin, Andrea; Lazzari, Gioele; Adriaenssens, Evelien M.; Vitulo, Nicola (2022). "Meta Phage: An Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data". mSystems. 7 (5): e0074122. doi:10.1128/msystems.00741-22. PMC 9599279. PMID 36069454.
  42. ^ Gauthier, Marie-Emilie A.; Lelwala, Ruvini V.; Elliott, Candace E.; Windell, Craig; Fiorito, Sonia; Dinsdale, Adrian; Whattam, Mark; Pattemore, Julie; Barrero, Roberto A. (2022). "Side-by-Side Comparison of Post-Entry Quarantine and High Throughput Sequencing Methods for Virus and Viroid Diagnosis". Biology. 11 (2): 263. doi:10.3390/biology11020263. PMC 8868628. PMID 35205129.
  43. ^ Brandt, Christian; Krautwurst, Sebastian; Spott, Riccardo; Lohde, Mara; Jundzill, Mateusz; Marquet, Mike; Hölzer, Martin (2021). "Pore Cov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction via Nanopore Sequencing". Frontiers in Genetics. 12: 711437. doi:10.3389/fgene.2021.711437. PMC 8355734. PMID 34394197.
  44. ^ Afiahayati; Bernard, Stefanus; Gunadi; Wibawa, Hendra; Hakim, Mohamad Saifudin; Marcellus; Parikesit, Arli Aditya; Dewa, Chandra Kusuma; Sakakibara, Yasubumi (2022). "A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains". Genes. 13 (8): 1330. doi:10.3390/genes13081330. PMC 9394340. PMID 35893066.
  45. ^ Niehaus, Jason (14 July 2022). "Bioinformatics at Addgene". Addgene corporate blog. Retrieved 25 February 2023.
  46. ^ Ssekagiri, Alfred; Jjingo, Daudi; Lujumba, Ibra; Bbosa, Nicholas; Bugembe, Daniel L.; Kateete, David P.; Jordan, I King; Kaleebu, Pontiano; Ssemwanga, Deogratius (2022). "Quasi Flow: A Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data". Bioinformatics Advances. 2: vbac089. doi:10.1093/bioadv/vbac089. PMC 9722223. PMID 36699347.
  47. ^ Theaud, Guillaume; Houde, Jean-Christophe; Boré, Arnaud; Rheault, François; Morency, Felix; Descoteaux, Maxime (2020). "Tracto Flow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity". NeuroImage. 218: 116889. doi:10.1016/j.neuroimage.2020.116889. PMID 32447016. S2CID 164318811.
  48. ^ Van Maldegem, Febe; Valand, Karishma; Cole, Megan; Patel, Harshil; Angelova, Mihaela; Rana, Sareena; Colliver, Emma; Enfield, Katey; Bah, Nourdine; Kelly, Gavin; Tsang, Victoria Siu Kwan; Mugarza, Edurne; Moore, Christopher; Hobson, Philip; Levi, Dina; Molina-Arcas, Miriam; Swanton, Charles; Downward, Julian (2021). "Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry". Nature Communications. 12 (1): 5906. Bibcode:2021NatCo..12.5906V. doi:10.1038/s41467-021-26214-x. PMC 8501076. PMID 34625563.
  49. ^ Li, Chenxin; Gao, Mingxuan; Yang, Wenxian; Zhong, Chuanqi; Yu, Rongshan (2021). "Diamond: A multi-modal DIA mass spectrometry data processing pipeline". Bioinformatics. 37 (2): 265–267. doi:10.1093/bioinformatics/btaa1093. PMID 33416868.
  50. ^ Luu, Gordon T.; Freitas, Michael A.; Lizama-Chamu, Itzel; McCaughey, Catherine S.; Sanchez, Laura M.; Wang, Mingxun (2022). "TIMSCONVERT: A workflow to convert trapped ion mobility data to open data formats". Bioinformatics. 38 (16): 4046–4047. doi:10.1093/bioinformatics/btac419. PMC 9991885. PMID 35758608.
  51. ^ Perez-Riverol, Yasset; Moreno, Pablo (2020). "Scalable Data Analysis in Proteomics and Metabolomics Using Bio Containers and Workflows Engines". Proteomics. 20 (9): e1900147. doi:10.1002/pmic.201900147. PMC 7613303. PMID 31657527.
  52. ^ Vlasova, Anna; Hermoso Pulido, Toni; Camara, Francisco; Ponomarenko, Julia; Guigó, Roderic (2021). "FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow". Genes. 12 (10): 1645. doi:10.3390/genes12101645. PMC 8535801. PMID 34681040.
  53. ^ Miller, Rachel M.; Jordan, Ben T.; Mehlferber, Madison M.; Jeffery, Erin D.; Chatzipantsiou, Christina; Kaur, Simi; Millikin, Robert J.; Dai, Yunxiang; Tiberi, Simone; Castaldi, Peter J.; Shortreed, Michael R.; Luckey, Chance John; Conesa, Ana; Smith, Lloyd M.; Deslattes Mays, Anne; Sheynkman, Gloria M. (2022). "Enhanced protein isoform characterization through long-read proteogenomics". Genome Biology. 23 (1): 69. doi:10.1186/s13059-022-02624-y. PMC 8892804. PMID 35241129.
  54. ^ Othman, Houcemeddine; Jemimah, Sherlyn; Da Rocha, Jorge Emanuel Batista (2022). "SWAAT Bioinformatics Workflow for Protein Structure-Based Annotation of ADME Gene Variants". Journal of Personalized Medicine. 12 (2): 263. doi:10.3390/jpm12020263. PMC 8875676. PMID 35207751.
  55. ^ Bichmann, Leon; Gupta, Shubham; Rosenberger, George; Kuchenbecker, Leon; Sachsenberg, Timo; Ewels, Phil; Alka, Oliver; Pfeuffer, Julianus; Kohlbacher, Oliver; Röst, Hannes (2021). "DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics". Journal of Proteome Research. 20 (7): 3758–3766. doi:10.1021/acs.jproteome.1c00123. PMID 34153189. S2CID 235597603.
  56. ^ Walzer, Mathias; García-Seisdedos, David; Prakash, Ananth; Brack, Paul; Crowther, Peter; Graham, Robert L.; George, Nancy; Mohammed, Suhaib; Moreno, Pablo; Papatheodorou, Irene; Hubbard, Simon J.; Vizcaíno, Juan Antonio (2022). "Implementing the reuse of public DIA proteomics datasets: From the PRIDE database to Expression Atlas". Scientific Data. 9 (1): 335. Bibcode:2022NatSD...9..335W. doi:10.1038/s41597-022-01380-9. PMC 9197839. PMID 35701420.
  57. ^ Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo; Walzer, Mathias; Barsnes, Harald; Martens, Lennart; Perez-Riverol, Yasset (2020). "ThermoRawFile Parser: Modular, Scalable, and Cross-Platform RAW File Conversion". Journal of Proteome Research. 19 (1): 537–542. doi:10.1021/acs.jproteome.9b00328. PMC 7116465. PMID 31755270.
  58. ^ Li, Kai; Jain, Antrix; Malovannaya, Anna; Wen, Bo; Zhang, Bing (2020). "Deep Rescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics". Proteomics. 20 (21–22): e1900334. doi:10.1002/pmic.201900334. PMC 7718998. PMID 32864883.
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See also

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Galaxy Snakemake