From ed964e94bd9cd7ca27334f6dfc6700ca8f9bd0d1 Mon Sep 17 00:00:00 2001 From: Alex Kanitz Date: Sat, 24 Aug 2024 17:22:48 +0200 Subject: [PATCH] chore: add CITATION.cff (#91) --- CITATION.cff | 344 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 344 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..cb6420a --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,344 @@ +# This CITATION.cff file was formatted with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! + +cff-version: 1.2.0 +title: ZARP-cli +message: >- + Please cite this software using the metadata from + 'preferred-citation'. +type: software +authors: + - affiliation: 'Biozentrum, University of Basel' + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' + - affiliation: 'Biozentrum, University of Basel' + family-names: Herrmann + given-names: Christina J. + orcid: 'https://orcid.org/0000-0003-1649-3463' + - affiliation: 'Biozentrum, University of Basel' + family-names: Bąk + given-names: Maciej + orcid: 'https://orcid.org/0000-0003-1361-7301' + - affiliation: 'Biozentrum, University of Basel' + family-names: Katsantoni + given-names: Maria + orcid: 'https://orcid.org/0000-0003-1961-0223' + - affiliation: 'Biozentrum, University of Basel' + family-names: Burri + given-names: Dominik + orcid: 'https://orcid.org/0000-0002-8131-9309' + - affiliation: 'Biozentrum, University of Basel' + family-names: Balajti + given-names: Máté + orcid: 'https://orcid.org/0009-0000-3932-3964' + - affiliation: 'Biozentrum, University of Basel' + family-names: Zavolan + given-names: Mihaela + orcid: 'https://orcid.org/0000-0002-8832-2041' +identifiers: + - type: doi + value: 10.5281/zenodo.10789818 + description: >- + Collection of archived snapshots of all versions of + ZARP-cli + - type: doi + value: 10.5281/zenodo.10789819 + description: >- + Archived snapshot of version v1.0.0-rc.1 of My + Research Software +repository-code: 'https://github.com/zavolanlab/zarp-cli' +url: 'https://zavolanlab.github.io/zarp-cli/' +abstract: >- + A user-friendly command-line interface for the ZARP + RNA-seq analysis workflow. +keywords: + - bioinformatics + - cli + - command-line-interface + - fair + - high-throughput + - library + - pipeline + - python + - reproducible-research + - rna-seq + - sequencing + - transcriptomics + - workflow +license: Apache-2.0 +commit: 4f861767029905ae543d7eb6d9772cae457e3f00 +version: v1.0.0-rc.1 +date-released: '2024-03-06' +contact: + - address: Spitalstrasse 41 + city: Basel + country: CH + email: zavolab-biozentrum@unibas.ch + location: 'Biozentrum, room 08.004' + name: 'Zavolab, Biozentrum, University of Basel' + post-code: 4056 + region: Basel-Stadt + website: >- + https://www.biozentrum.unibas.ch/research/research-groups/research-groups-a-z/overview/unit/research-group-mihaela-zavolan + - affiliation: 'Biozentrum, University of Basel' + email: alexander.kanitz@alumni.ethz.ch + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' +preferred-citation: + abstract: >- + BACKGROUND: RNA sequencing (RNA-seq) is a widely used technique in many + scientific studies. Given the plethora of models and software packages that + have been developed for processing and analyzing RNA-seq datasets, choosing + the most appropriate ones is a time-consuming process that requires an + in-depth understanding of the data, as well as of the principles and + parameters of each tool. In addition, packages designed for individual tasks + are developed in different programming languages and have dependencies of + various degrees of complexity, which renders their installation and + execution challenging for users with limited computational expertise. + Workflow languages and execution engines with support for virtualization and + encapsulation options such as containers and Conda environments facilitate + these tasks considerably. The resulting computational workflows can then be + reliably shared with the scientific community, enhancing reusability and the + reproducibility of results as individual analysis steps are becoming more + transparent and portable. METHODS: Here we present ZARP, a general purpose + RNA-seq analysis workflow that builds on state-of-the-art software in the + field to facilitate the analysis of RNA-seq datasets. ZARP is developed in + the Snakemake workflow language and can run locally or in a cluster + environment, generating extensive reports not only of the data but also of + the options utilized. It is built using modern technologies with the + ultimate goal to reduce the hands-on time for bioinformaticians and + non-expert users and serve as a template for future workflow development. To + this end, we also provide ZARP-cli, a dedicated command-line interface that + may make running ZARP on an RNA-seq library of interest as easy as executing + a single two-word command. CONCLUSIONS: ZARP is a powerful RNA-seq analysis + workflow that is easy to use even for beginners, built using best software + development practices, available under a permissive Open Source license and + open to contributions by the scientific community. + authors: + - affiliation: 'Biozentrum, University of Basel' + family-names: Katsantoni + given-names: Maria + orcid: 'https://orcid.org/0000-0003-1961-0223' + - affiliation: 'Biozentrum, University of Basel' + family-names: Gypas + given-names: Foivos + orcid: 'https://orcid.org/0000-0002-7233-8794' + - affiliation: 'Biozentrum, University of Basel' + family-names: Herrmann + given-names: Christina J. + orcid: 'https://orcid.org/0000-0003-1649-3463' + - affiliation: 'Biozentrum, University of Basel' + family-names: Burri + given-names: Dominik + orcid: 'https://orcid.org/0000-0002-8131-9309' + - affiliation: 'Biozentrum, University of Basel' + family-names: Bąk + given-names: Maciej + orcid: 'https://orcid.org/0000-0003-1361-7301' + - affiliation: 'Biozentrum, University of Basel' + family-names: Iborra + given-names: Paula + orcid: 'https://orcid.org/0000-0003-0504-3029' + - affiliation: 'Biozentrum, University of Basel' + family-names: Agarwal + given-names: Krish + orcid: 'https://orcid.org/0000-0001-6809-5024' + - affiliation: 'Biozentrum, University of Basel' + family-names: Ataman + given-names: Meriç + orcid: 'https://orcid.org/0000-0002-7942-9226' + - affiliation: 'Biozentrum, University of Basel' + family-names: Balajti + given-names: Máté + orcid: 'https://orcid.org/0009-0000-3932-3964' + - affiliation: 'Biozentrum, University of Basel' + family-names: Pozzan + given-names: Noè + orcid: 'https://orcid.org/0009-0007-0466-8269' + - affiliation: 'Biozentrum, University of Basel' + family-names: Schlusser + given-names: Niels + orcid: 'https://orcid.org/0000-0002-3534-2153' + - affiliation: 'Biozentrum, University of Basel' + family-names: Moon + given-names: Youngbin + orcid: 'https://orcid.org/0009-0001-5728-3959' + - affiliation: 'Biozentrum, University of Basel' + family-names: Mironov + given-names: Aleksei + orcid: 'https://orcid.org/0000-0003-4228-7022' + - affiliation: 'Biozentrum, University of Basel' + family-names: Börsch + given-names: Anastasiya + orcid: 'https://orcid.org/0000-0003-3392-5272' + - affiliation: 'Biozentrum, University of Basel' + family-names: Zavolan + given-names: Mihaela + orcid: 'https://orcid.org/0000-0002-8832-2041' + - affiliation: 'Biozentrum, University of Basel' + country: CH + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' + contact: + - address: Spitalstrasse 41 + city: Basel + country: CH + email: zavolab-biozentrum@unibas.ch + location: 'Biozentrum, room 08.004' + name: 'Zavolab, Biozentrum, University of Basel' + post-code: 4056 + region: Basel-Stadt + website: >- + https://www.biozentrum.unibas.ch/research/research-groups/research-groups-a-z/overview/unit/research-group-mihaela-zavolan + - affiliation: 'Biozentrum, University of Basel' + email: alexander.kanitz@unibas.ch + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' + - affiliation: 'Biozentrum, University of Basel' + email: mihaela.zavolan@unibas.ch + family-names: Zavolan + given-names: Mihaela + orcid: 'https://orcid.org/0000-0002-8832-2041' + copyright: © 2024 Katsantoni M et al. + date-published: '2024-05-24' + department: Biozentrum + doi: 10.12688/f1000research.149237.1 + institution: + name: University of Basel + issn: 2046-1402 + journal: F1000Research + keywords: + - bioinformatics + - computational workflow + - data analysis + - high-throughput + - reproducibility + - RNA-seq + - transcriptomics + - usability + languages: + - en + license: CC-BY-4.0 + month: 5 + notes: Article describing the ZARP workflow and its command-line interface ZARP-cli. + number: 533 + publisher: + name: F1000 Research Ltd + status: preprint + title: 'ZARP: A user-friendly and versatile RNA-seq analysis workflow' + type: article + url: 'https://f1000research.com/articles/13-533/v1' + version: 1 + volume: 13 + year: 2024 +references: + - authors: + - name: genomepy team + doi: 10.5281/zenodo.1010458 + license: MIT + repository-code: 'https://github.com/vanheeringen-lab/genomepy' + title: genomepy + type: software + url: 'https://vanheeringen-lab.github.io/genomepy/' + - authors: + - affiliation: 'Biozentrum, University of Basel' + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' + - affiliation: 'Biozentrum, University of Basel' + family-names: Balajti + given-names: Máté + orcid: 'https://orcid.org/0009-0000-3932-3964' + - affiliation: 'Biozentrum, University of Basel' + family-names: Kandari + given-names: Rohan + - affiliation: 'Institute of Computer Science, Masaryk University' + family-names: Jurič + given-names: Boris + - affiliation: 'Biozentrum, University of Basel' + family-names: Herrmann + given-names: Christina J. + orcid: 'https://orcid.org/0000-0003-1649-3463' + - affiliation: 'Biozentrum, University of Basel' + family-names: How + given-names: Hiap Chon + - affiliation: 'Biozentrum, University of Basel' + family-names: Bąk + given-names: Maciej + orcid: 'https://orcid.org/0000-0003-1361-7301' + license: Apache-2.0 + repository-code: 'https://github.com/zavolanlab/htsinfer' + title: HTSinfer + type: software + - authors: + - name: Snakemake team + license: MIT + repository-code: 'https://github.com/snakemake/snakemake' + title: Snakemake + type: software + url: 'https://snakemake.github.io/' + - authors: + - name: SRA Tools team + license-url: >- + https://github.com/ncbi/sra-tools/blob/0cf634c2fb641cd55c6bff987c95ac669273eea9/LICENSE + repository-code: 'https://github.com/ncbi/sra-tools' + title: SRA Tools + type: software + - authors: + - affiliation: 'Biozentrum, University of Basel' + family-names: Katsantoni + given-names: Maria + orcid: 'https://orcid.org/0000-0003-1961-0223' + - affiliation: 'Biozentrum, University of Basel' + family-names: Kanitz + given-names: Alexander + orcid: 'https://orcid.org/0000-0002-3468-0652' + - affiliation: 'Biozentrum, University of Basel' + family-names: Herrmann + given-names: Christina J. + orcid: 'https://orcid.org/0000-0003-1649-3463' + - affiliation: 'Biozentrum, University of Basel' + family-names: Burri + given-names: Dominik + orcid: 'https://orcid.org/0000-0002-8131-9309' + - affiliation: 'Biozentrum, University of Basel' + family-names: Gypas + given-names: Foivos + orcid: 'https://orcid.org/0000-0002-7233-8794' + - affiliation: 'Biozentrum, University of Basel' + family-names: Bąk + given-names: Maciej + orcid: 'https://orcid.org/0000-0003-1361-7301' + - affiliation: 'Biozentrum, University of Basel' + family-names: Balajti + given-names: Máté + orcid: 'https://orcid.org/0009-0000-3932-3964' + - affiliation: 'Biozentrum, University of Basel' + family-names: Pozzan + given-names: Noè + orcid: 'https://orcid.org/0009-0007-0466-8269' + - affiliation: 'Biozentrum, University of Basel' + family-names: Ataman + given-names: Meriç + orcid: 'https://orcid.org/0000-0002-7942-9226' + - affiliation: 'Biozentrum, University of Basel' + family-names: Zavolan + given-names: Mihaela + orcid: 'https://orcid.org/0000-0002-8832-2041' + - affiliation: 'Biozentrum, University of Basel' + family-names: Schlusser + given-names: Niels + orcid: 'https://orcid.org/0000-0002-3534-2153' + - affiliation: 'Biozentrum, University of Basel' + family-names: Mironov + given-names: Aleksei + orcid: 'https://orcid.org/0000-0003-4228-7022' + license: Apache-2.0 + repository-code: 'https://github.com/zavolanlab/htsinfer' + title: ZARP + type: software + url: 'https://zavolanlab.github.io/zarp/'