From 15d8ac5b4b531175da823447663ce8fa01ae8ef1 Mon Sep 17 00:00:00 2001 From: Jannik Seidel Date: Mon, 19 Feb 2024 13:12:19 +0100 Subject: [PATCH] updated citations --- CITATIONS.md | 12 ++++++++++++ README.md | 2 -- assets/methods_description_template.yml | 2 -- lib/WorkflowDetaxizer.groovy | 23 ++++++++++++----------- 4 files changed, 24 insertions(+), 15 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 4d08475..ddff8d5 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -30,6 +30,18 @@ > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. +- [seqkit](https://bioinf.shenwei.me/seqkit/) + + > Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. In Q. Zou (Ed.), PLOS ONE (Vol. 11, Issue 10, p. e0163962). Public Library of Science (PLoS). doi:10.1371/journal.pone.0163962 + +## Python + +- [Python](https://www.python.org/) + +- [biopython](https://biopython.org/) + + > Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., & de Hoon, M. J. L. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. In Bioinformatics (Vol. 25, Issue 11, pp. 1422–1423). Oxford University Press (OUP). doi:10.1093/bioinformatics/btp163 + ## Software packaging/containerisation tools - [Anaconda](https://anaconda.com) diff --git a/README.md b/README.md index 0f2aa46..46c85c9 100644 --- a/README.md +++ b/README.md @@ -86,8 +86,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `# - - An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. You can cite the `nf-core` publication as follows: diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 8956ed8..b7c67e5 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -3,8 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag section_name: "nf-core/detaxizer Methods Description" section_href: "https://github.com/nf-core/detaxizer" plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

Data was processed using nf-core/detaxizer v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

diff --git a/lib/WorkflowDetaxizer.groovy b/lib/WorkflowDetaxizer.groovy index c5e8fa9..e6c5441 100755 --- a/lib/WorkflowDetaxizer.groovy +++ b/lib/WorkflowDetaxizer.groovy @@ -53,13 +53,14 @@ class WorkflowDetaxizer { public static String toolCitationText(params) { - // TODO nf-core: Optionally add in-text citation tools to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", "FastQC (Andrews 2010),", - "MultiQC (Ewels et al. 2016)", + "MultiQC (Ewels et al. 2016),", + "Kraken2 (Wood et al. 2019),", + !params["skip_blastn"] ? "BLAST (Altschul et al. 1990)," : "", + !params["skip_blastn"] | params["enable_filter"] ? "seqkit (Shen et al. 2016)," : "", + "fastp (Chen et al. 2018)", "." ].join(' ').trim() @@ -68,12 +69,13 @@ class WorkflowDetaxizer { public static String toolBibliographyText(params) { - // TODO Optionally add bibliographic entries to this list. - // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "
  • Author (2023) Pub name, Journal, DOI
    • " : "", - // Uncomment function in methodsDescriptionText to render in MultiQC report def reference_text = [ "
  • Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
    • ", - "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • " + "
  • Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354
    • ", + "
  • Wood, D. E., Lu, J. & Langmead, B. (2019) Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257. doi: 10.1186/s13059-019-1891-0
    • ", + !params["skip_blastn"] ? "
  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410. doi: 10.1016/s0022-2836(05)80360-2.
    • " : "", + !params["skip_blastn"] | params["enable_filter"] ? "
  • Shen, W., Le, S., Li, Y., & Hu, F. (2016). SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. In Q. Zou (Ed.), PLOS ONE (Vol. 11, Issue 10, p. e0163962). Public Library of Science (PLoS). doi: 10.1371/journal.pone.0163962
    • " : "", + "
  • Chen, S., Zhou, Y., Chen, Y. & Gu, J. (2018) fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890. doi: 10.1093/bioinformatics/bty560
    • " ].join(' ').trim() return reference_text @@ -93,9 +95,8 @@ class WorkflowDetaxizer { meta["tool_citations"] = "" meta["tool_bibliography"] = "" - // TODO Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! - //meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") - //meta["tool_bibliography"] = toolBibliographyText(params) + meta["tool_citations"] = toolCitationText(params).replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".") + meta["tool_bibliography"] = toolBibliographyText(params) def methods_text = mqc_methods_yaml.text