diff --git a/subworkflows/local/utils_nfcore_molkart_pipeline/main.nf b/subworkflows/local/utils_nfcore_molkart_pipeline/main.nf index 005bf96..8a2e278 100644 --- a/subworkflows/local/utils_nfcore_molkart_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_molkart_pipeline/main.nf @@ -170,7 +170,7 @@ def toolCitationText() { // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ "Tools used in the workflow included:", - "Mindagap (Guerreiro et al. 2023),", + params.skip_mindagap ? "" : "Mindagap (Guerreiro et al. 2023),", params.segmentation_method.split(',').contains('mesmer') ? "Mesmer (Greenwald et al. 2021)," : "", params.segmentation_method.split(',').contains('ilastik') ? "ilastik (Berg et al. 2019)," : "", params.segmentation_method.split(',').contains('cellpose') ? "Cellpose (Stringer et al. 2021; Pachitariu et al 2022)," : "", @@ -184,7 +184,7 @@ def toolBibliographyText() { // 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 = [ - "
  • Ricardo Guerreiro, Florian Wuennemann, & pvtodorov. (2023). ViriatoII/MindaGap: v0.0.3 (0.0.3). Zenodo. https://doi.org/10.5281/zenodo.8120559", + params.skip_mindagap ? "" : "
  • Ricardo Guerreiro, Florian Wuennemann, & pvtodorov. (2023). ViriatoII/MindaGap: v0.0.3 (0.0.3). Zenodo. https://doi.org/10.5281/zenodo.8120559", params.segmentation_method.split(',').contains('mesmer') ? "
  • Greenwald, N.F., Miller, G., Moen, E. et al. Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning. Nat Biotechnol 40, 555–565 (2022). https://doi.org/10.1038/s41587-021-01094-0
  • " : "", params.segmentation_method.split(',').contains('ilastik') ? "
  • Berg, S., Kutra, D., Kroeger, T. et al. ilastik: interactive machine learning for (bio)image analysis. Nat Methods 16, 1226–1232 (2019). https://doi.org/10.1038/s41592-019-0582-9
  • " : "", params.segmentation_method.split(',').contains('cellpose') ? "
  • Stringer, C., Wang, T., Michaelos, M. et al. Cellpose: a generalist algorithm for cellular segmentation. Nat Methods 18, 100–106 (2021). https://doi.org/10.1038/s41592-020-01018-x
  • " : "",