applying reviewer suggestions on #117

nf-core · Mar 19, 2024 · 5ceb33c · 5ceb33c
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Showing 2 changed files with 33 additions and 6 deletions.
diff --git a/main.nf b/main.nf
@@ -21,9 +21,6 @@ include { BACASS  } from './workflows/bacass'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_bacass_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_bacass_pipeline'
 
-include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_bacass_pipeline'
-
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE

diff --git a/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf b/subworkflows/local/utils_nfcore_bacass_pipeline/main.nf
@@ -203,6 +203,21 @@ def toolCitationText() {
     def citation_text = [
             "Tools used in the workflow included:",
             "FastQC (Andrews 2010),",
+            "ProeChop (Wick RR et al. 2017)",
+            "Nanoplot (Wouter De Coster and Rosa Rademakers 2023)",
+            "PycoQC (Adrien Leger & Tommaso Leonardi 2019)",
+            "Kreken2 (Derrick E. Wood et al. 2019)",
+            "Unicycler (Ryan R Wick et al. 2017)",
+            "Minimap & Miniasm (Heng Li 2016)",
+            "Dragonflye (Robert A Petit III )",
+            "Racon (Vaser R et al. 2017)",
+            "Canu (Sergey Koren et al. 2017)",
+            "Medaka (Heng Li)",
+            "Nanopolish (Loman 2015)",
+            "Quast (Alexey Gurevich et al. 2013)",
+            "Prokka (Torsten Seemann 2014)",
+            "Bakta (Oliver Schwengers 2021)",
+            "Dfast(Yasuhiro Tanizawa et al. 2018)",
             "MultiQC (Ewels et al. 2016)",
             "."
         ].join(' ').trim()
@@ -216,6 +231,21 @@ def toolBibliographyText() {
     // 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>Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom. 2017;3(10):e000132. Published 2017 Sep 14. doi:10.1099/mgen.0.000132</li>",
+            "<li>Wouter De Coster, Rosa Rademakers, NanoPack2: population-scale evaluation of long-read sequencing data, Bioinformatics, Volume 39, Issue 5, May 2023, btad311, https://doi.org/10.1093/bioinformatics/btad311</li>",
+            "<li>Leger et al., (2019). pycoQC, interactive quality control for Oxford Nanopore Sequencing. Journal of Open Source Software, 4(34), 1236, https://doi.org/10.21105/joss.01236</li>",
+            "<li>Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0</li>",
+            "<li>Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017 Jun 8;13(6):e1005595. doi: 10.1371/journal.pcbi.1005595.</li>",
+            "<li>Heng Li, Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences, Bioinformatics, Volume 32, Issue 14, July 2016, Pages 2103–2110, https://doi.org/10.1093/bioinformatics/btw152</li>",
+            "<li>[rpetit/dragonflye](https://github.com/rpetit3/dragonflye)</li>",
+            "<li>Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017 May;27(5):737-746. doi: 10.1101/gr.214270.116.</li>",
+            "<li>Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017 May;27(5):722-736. doi: 10.1101/gr.215087.116.</li>",
+            "<li>Medaka: Sequence correction provided by ONT Research. https://github.com/nanoporetech/medaka,</li>",
+            "<li>Loman, N., Quick, J. & Simpson, J. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods 12, 733–735 (2015). https://doi.org/10.1038/nmeth.3444</li>",
+            "<li>Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19.</li>",
+            "<li>Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014 Jul 15;30(14):2068-9. doi: 10.1093/bioinformatics/btu153.</li>",
+            "<li>Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genom. 2021 Nov;7(11):000685. doi: 10.1099/mgen.0.000685.</li>",
+            "<li>Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics. 2018 Mar 15;34(6):1037-1039. doi: 10.1093/bioinformatics/btx713.</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>"
         ].join(' ').trim()
 
@@ -236,9 +266,9 @@ 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()
+    // Tool citations and bibliography
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text