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Address Make citation tools dependent on whether tool was executed #468
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atrigila committed Oct 8, 2024
1 parent 1ed464e commit 48337c8
Showing 1 changed file with 7 additions and 8 deletions.
15 changes: 7 additions & 8 deletions subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -220,23 +220,22 @@ def toolCitationText() {
// 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),",
!params.skip_fastqc ? "FastQC (Andrews 2010)," : "",
!params.skip_multiqc ? "MultiQC (Ewels et al. 2016)," : "",
!params.skip_fastp ? "fastp (Chen et al. 2018)," : "",
!params.skip_mirdeep ? "MiRDeep2 (Friedländer et al. 2012)," : "",
params.filter_contamination ? "Contamination filtering tools: BLAT (Kent 2002), Bowtie2 (Langmead and Salzberg 2012)," : "",
params.mirtrace_species ? "miRTrace (Kang et al. 2018)," : "",
"UMI-tools (Smith et al. 2017),",
"fastp (Chen et al. 2018),",
"miRTrace (Kang et al. 2018),",
"Bowtie (Langmead et al. 2009),",
"Bowtie2 (Langmead and Salzberg 2012),",
"SAMtools (Li et al. 2009),",
"EdgeR (Robinson et al. 2010),",
"Mirtop (Desvignes et al. 2019),",
"MiRDeep2 (Friedländer et al. 2012),",
"SeqKit (Shen et al. 2016),",
"UMICollapse (Liu 2020),",
"BLAT (Kent 2002)",
"Seqcluster (Pantano et al. 2011)",
"."
].join(' ').trim()
].join(' ').trim()

return citation_text
}
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