Merge branch 'dev' into nf-core-template-merge-3.1.1

.github/workflows/ci.yml

@@ -34,7 +34,7 @@ jobs:
           - "docker"
           - "singularity"
         test_name:
-          - "test"
+          - "test_stub"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev
@@ -82,4 +82,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -stub -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results

.gitignore

@@ -1,3 +1,5 @@
+examples/
+*.tar.gz
 .nextflow*
 work/
 data/

CHANGELOG.md

@@ -1,16 +1,15 @@
 # nf-core/oncoanalyser: Changelog
 
-The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
-and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project mostly adheres to
+[Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v1.1.0dev - [date]
+## [dev]
 
-Initial release of nf-core/oncoanalyser, created with the [nf-core](https://nf-co.re/) template.
-
-### `Added`
+- [105](https://github.com/nf-core/oncoanalyser/pull/105) - Adjust MarkDups outputs to improve efficiency with k8s
+- [98](https://github.com/nf-core/oncoanalyser/pull/98) - Fix typos in error messages for process and run mode check
+- [96](https://github.com/nf-core/oncoanalyser/pull/96) - Added missing type field to an entry in the nextflow_schema.json
+- [95](https://github.com/nf-core/oncoanalyser/pull/95) - Post-release bump
 
-### `Fixed`
+## [[1.0.0](https://github.com/nf-core/oncoanalyser/releases/tag/1.0.0)] Pied Currawong - 2024-08-26
 
-### `Dependencies`
-
-### `Deprecated`
+Initial release of nf-core/oncoanalyser, created with the [nf-core](https://nf-co.re/) template.

CITATIONS.md

@@ -10,30 +10,80 @@
 
 ## Pipeline tools
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [BCFtools](https://doi.org/10.1093/gigascience/giab008)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> 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
 
-> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+- [BWA](https://doi.org/10.1093/bioinformatics/btp324)
+
+> Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760. https://doi.org/10.1093/bioinformatics/btp324
+
+- [bwa-mem2](https://doi.org/10.1109/IPDPS.2019.00041)
+
+> Vasimuddin, Md., Misra, S., Li, H., & Aluru, S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 314–324. https://doi.org/10.1109/IPDPS.2019.00041
+
+- [CHORD](https://doi.org/10.1038/s41467-020-19406-4)
+
+> Nguyen, L., W. M. Martens, J., Van Hoeck, A., & Cuppen, E. (2020). Pan-cancer landscape of homologous recombination deficiency. Nature Communications, 11(1), 5584. https://doi.org/10.1038/s41467-020-19406-4
+
+- [fastp](https://doi.org/10.1093/bioinformatics/bty560)
+
+> Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics, 34(17), i884–i890. https://doi.org/10.1093/bioinformatics/bty560
+
+- [GATK](https://doi.org/10.1093/bioinformatics/btp324)
+
+> 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
+
+- [GRIDSS2](https://doi.org/10.1186/s13059-021-02423-x)
+
+> Cameron, D. L., Baber, J., Shale, C., Valle-Inclan, J. E., Besselink, N., van Hoeck, A., Janssen, R., Cuppen, E., Priestley, P., & Papenfuss, A. T. (2021). GRIDSS2: Comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing. Genome Biology, 22(1), Article 1. https://doi.org/10.1186/s13059-021-02423-x
+
+- [LILAC](https://doi.org/10.1038/s41588-023-01367-1)
+
+> Martínez-Jiménez, F., Priestley, P., Shale, C., Baber, J., Rozemuller, E., & Cuppen, E. (2023). Genetic immune escape landscape in primary and metastatic cancer. Nature Genetics, 55(5), 820–831. https://doi.org/10.1038/s41588-023-01367-1
+
+- [LINX](https://doi.org/10.1016/j.xgen.2022.100112)
+
+> Shale, C., Cameron, D. L., Baber, J., Wong, M., Cowley, M. J., Papenfuss, A. T., Cuppen, E., & Priestley, P. (2022). Unscrambling cancer genomes via integrated analysis of structural variation and copy number. Cell Genomics, 2(4). https://doi.org/10.1016/j.xgen.2022.100112
+
+- [PURPLE](https://doi.org/10.1038/s41586-019-1689-y)
+
+> Priestley, P., Baber, J., Lolkema, M. P., Steeghs, N., de Bruijn, E., Shale, C., Duyvesteyn, K., Haidari, S., van Hoeck, A., Onstenk, W., Roepman, P., Voda, M., Bloemendal, H. J., Tjan-Heijnen, V. C. G., van Herpen, C. M. L., Labots, M., Witteveen, P. O., Smit, E. F., Sleijfer, S., … Cuppen, E. (2019). Pan-cancer whole-genome analyses of metastatic solid tumours. Nature, 575(7781), 210–216. https://doi.org/10.1038/s41586-019-1689-y
+
+- [Sambamba](https://doi.org/10.1093/bioinformatics/btv098)
+
+> Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015). Sambamba: Fast processing of NGS alignment formats. Bioinformatics, 31(12), 2032–2034. https://doi.org/10.1093/bioinformatics/btv098
+
+- [SAMtools](https://doi.org/10.1093/gigascience/giab008)
+
+> 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
+
+- [STAR](https://doi.org/10.1093/bioinformatics/bts635)
+
+> Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15–21. https://doi.org/10.1093/bioinformatics/bts635
+
+- [VIRUSBreakend](https://doi.org/10.1093/bioinformatics/btab343)
+
+> Cameron, D. L., Jacobs, N., Roepman, P., Priestley, P., Cuppen, E., & Papenfuss, A. T. (2021). VIRUSBreakend: Viral Integration Recognition Using Single Breakends. Bioinformatics, 37(19), 3115–3119. https://doi.org/10.1093/bioinformatics/btab343
 
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+> Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
 
 - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 
-  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+> Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
 - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 
-  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+> da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
-  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
 
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
 
-  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.