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Added citations to utils_nfcore_detaxizer_pipeline/main.nf #18

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merged 2 commits into from
Mar 6, 2024
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Added citations to utils_nfcore_detaxizer_pipeline/main.nf #18

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Added citations to utils_nfcore_detaxizer_pipeline/main.nf
jannikseidelQBiC Mar 5, 2024
ac3ea06
changed order of citations
jannikseidelQBiC Mar 5, 2024
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23 changes: 13 additions & 10 deletions subworkflows/local/utils_nfcore_detaxizer_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -182,26 +182,30 @@ def genomeExistsError() {
// Generate methods description for MultiQC
//
def toolCitationText() {
// 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)",
"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)",
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you could roughly keep the sequence of the tools, i.e. to put fastp right after FastQC or such.

"."
].join(' ').trim()

return citation_text
}

def toolBibliographyText() {
// TODO nf-core: Optionally add bibliographic entries to this list.
// Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
// Uncomment function in methodsDescriptionText to render in MultiQC report

def reference_text = [
"<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
"<li>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</li>"
"<li>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</li>",
"<li>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</li>",
!params["skip_blastn"] ? "<li>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.</li>" : "",
!params["skip_blastn"] | params["enable_filter"] ? "<li>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</li>" : "",
"<li>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</li>"
].join(' ').trim()

return reference_text
Expand All @@ -221,9 +225,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
meta["tool_citations"] = ""
meta["tool_bibliography"] = ""

// TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
// meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
// meta["tool_bibliography"] = toolBibliographyText()
meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
meta["tool_bibliography"] = toolBibliographyText()


def methods_text = mqc_methods_yaml.text
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