update citations

Author: ramprasadn

CHANGELOG.md

@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | skip_haplogrep3          | skip_tools    |
 | skip_fastp               |               |
 | skip_gens                |               |
+| skip_germlinecnvcaller   |               |
 | skip_peddy               |               |
 | skip_smncopynumbercaller |               |
 | skip_vcf2cytosure        |               |

subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf

@@ -426,7 +426,6 @@ def toolCitationText() {
             "VEP (McLaren et al., 2016),",
             "Vcfanno (Pedersen et al., 2016),",
             "Hmtnote (Preste et al., 2019),",
-            "HaploGrep2 (Weissensteiner et al., 2016),",
             "Genmod (Magnusson et al., 2018),"
         ]
         if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) {
@@ -457,14 +456,14 @@ def toolCitationText() {
     ]
     preprocessing_text = [
         "FastQC (Andrews 2010),",
-        params.skip_tools && params.skip_tools.split(',').contains('fastp') ? "" : "Fastp (Chen, 2023),"
+        (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "Fastp (Chen, 2023),"
     ]
     other_citation_text = [
         "BCFtools (Danecek et al., 2021),",
         "BEDTools (Quinlan & Hall, 2010),",
         "GATK (McKenna et al., 2010),",
         "MultiQC (Ewels et al. 2016),",
-        params.skip_tools && params.skip_tools.split(',').contains('peddy') ? "" : "Peddy (Pedersen & Quinlan, 2017),",
+        (params.skip_tools && params.skip_tools.split(',').contains('peddy')) ? "" : "Peddy (Pedersen & Quinlan, 2017),",
         params.run_rtgvcfeval ? "RTG Tools (Cleary et al., 2015)," : "",
         "SAMtools (Li et al., 2009),",
         (!(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) && params.analysis_type.equals("wgs")) ? "SMNCopyNumberCaller (Chen et al., 2020)," : "",
@@ -556,7 +555,6 @@ def toolBibliographyText() {
             "<li>Pedersen, B. S., Layer, R. M., & Quinlan, A. R. (2016). Vcfanno: Fast, flexible annotation of genetic variants. Genome Biology, 17(1), 118. https://doi.org/10.1186/s13059-016-0973-5</li>",
             "<li>McLaren, W., Gil, L., Hunt, S. E., Riat, H. S., Ritchie, G. R. S., Thormann, A., Flicek, P., & Cunningham, F. (2016). The Ensembl Variant Effect Predictor. Genome Biology, 17(1), 122. https://doi.org/10.1186/s13059-016-0974-4</li>",
             "<li>Preste, R., Clima, R., & Attimonelli, M. (2019). Human mitochondrial variant annotation with HmtNote [Preprint]. Bioinformatics. https://doi.org/10.1101/600619</li>",
-            "<li>Weissensteiner, H., Pacher, D., Kloss-Brandstätter, A., Forer, L., Specht, G., Bandelt, H.-J., Kronenberg, F., Salas, A., & Schönherr, S. (2016). HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Research, 44(W1), W58–W63. https://doi.org/10.1093/nar/gkw233</li>",
             "<li>Magnusson, M., Hughes, T., Glabilloy, & Bitdeli Chef. (2018). genmod: Version 3.7.3 (3.7.3) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3841142</li>"
         ]
         if (!(params.skip_tools && params.skip_tools.split(',').contains('haplogrep3'))) {
@@ -586,14 +584,14 @@ def toolBibliographyText() {
     ]
     preprocessing_text = [
         "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</li>",
-        params.skip_tools && params.skip_tools.split(',').contains('fastp') ? "" : "<li>Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107</li>"
+        (params.skip_tools && params.skip_tools.split(',').contains('fastp')) ? "" : "<li>Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107</li>"
     ]
 
     other_citation_text = [
         "<li>Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008</li>",
         "<li>McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303. https://doi.org/10.1101/gr.107524.110</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. https://doi.org/10.1093/bioinformatics/btw354</li>",
-        params.skip_tools && params.skip_tools.split(',').contains('peddy') ? "" : "<li>Pedersen, B. S., & Quinlan, A. R. (2017). Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. The American Journal of Human Genetics, 100(3), 406–413. https://doi.org/10.1016/j.ajhg.2017.01.017</li>",
+        (params.skip_tools && params.skip_tools.split(',').contains('peddy')) ? "" : "<li>Pedersen, B. S., & Quinlan, A. R. (2017). Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. The American Journal of Human Genetics, 100(3), 406–413. https://doi.org/10.1016/j.ajhg.2017.01.017</li>",
         params.run_rtgvcfeval ? "<li>Cleary, J. G., Braithwaite, R., Gaastra, K., Hilbush, B. S., Inglis, S., Irvine, S. A., Jackson, A., Littin, R., Rathod, M., Ware, D., Zook, J. M., Trigg, L., & Vega, F. M. D. L. (2015). Comparing Variant Call Files for Performance Benchmarking of Next-Generation Sequencing Variant Calling Pipelines (p. 023754). bioRxiv. https://doi.org/10.1101/023754</li>" : "",
         "<li>Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352</li>",
         (!(params.skip_tools && params.skip_tools.split(',').contains('smncopynumbercaller')) && params.analysis_type.equals("wgs")) ? "<li>Chen, X., Sanchis-Juan, A., French, C. E., Connell, A. J., Delon, I., Kingsbury, Z., Chawla, A., Halpern, A. L., Taft, R. J., Bentley, D. R., Butchbach, M. E. R., Raymond, F. L., & Eberle, M. A. (2020). Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genetics in Medicine, 22(5), 945–953. https://doi.org/10.1038/s41436-020-0754-0</li>" : "",