rm references bibtex

nf-core · Apr 27, 2022 · 73fa3df · 73fa3df
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diff --git a/assets/references.bibtex b/assets/references.bibtex
diff --git a/assets/repertoire_comparison.Rmd b/assets/repertoire_comparison.Rmd
@@ -12,11 +12,6 @@ output:
     pdf_document: true
   html_notebook:
     toc: yes
-params:
-  path_css: ""
-  path_logo: ""
-  path_bibliography: ""
-bibliography: '`r params$path_bibliography`'
 ---
 
 
@@ -501,13 +496,53 @@ write.table(family, file = paste0(vfamily_dir, "/V_gene_distribution_by_sequence
 
 If you use nf-core/airrflow for your analysis, please cite it using the following DOI: [10.5281/zenodo.3607408](https://doi.org/10.5281/zenodo.3607408)
 
-Please also cite the `nf-core` publication [@ewels2020].
+Please also cite the `nf-core` and `Nextflow` publications:
+
+- [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+  > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+- [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+  > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
 In addition, citations for the tools and data used in this pipeline are as follows:
 
-* **pRESTO** [@VanderHeiden2014]
-* **SHazaM, Change-O** [@Gupta2015]
-* **Alakazam** [@Stern2014]
-* **TIgGER** [@Gadala-Maria2015]
-* **FastQC** [@andrews2010]
-* **MultiQC** [@ewels2016]
+- [pRESTO](https://doi.org/10.1093/bioinformatics/btu138)
+
+  > Vander Heiden, J. A., Yaari, G., Uduman, M., Stern, J. N. H., O’Connor, K. C., Hafler, D. A., … Kleinstein, S. H. (2014). pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics, 30(13), 1930–1932.
+
+- [SHazaM, Change-O](https://doi.org/10.1093/bioinformatics/btv359)
+
+  > Gupta, N. T., Vander Heiden, J. A., Uduman, M., Gadala-Maria, D., Yaari, G., & Kleinstein, S. H. (2015). Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1. Bioinformatics, 31(20), 3356–3358.
+
+- [Alakazam](https://doi.org/10.1126/scitranslmed.3008879)
+
+  > Stern, J. N. H., Yaari, G., Vander Heiden, J. A., Church, G., Donahue, W. F., Hintzen, R. Q., … O’Connor, K. C. (2014). B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Science Translational Medicine, 6(248).
+
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
+  > 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.
+
+## Software packaging/containerisation tools
+
+- [Anaconda](https://anaconda.com)
+
+  > 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.
+
+- [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.
+
+- [Docker](https://dl.acm.org/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.
+
diff --git a/bin/execute_report.R b/bin/execute_report.R
@@ -4,18 +4,12 @@ library(rmarkdown)
 library(optparse)
 
 option_list = list(
-    make_option(c("-r", "--report_file"), type="character", default=NULL, help="report rmarkdown file", metavar="character"),
-    make_option(c("-b", "--references"), type="character", default=NULL, help="references bibtex file", metavar="character"),
-    make_option(c("-c","--css"), type ="character", default=NULL, help="css file for report formatting", metavar="character"),
-    make_option(c("-l","--logo"), type="character", default=NULL, help="logo for report", metavar="character")
+    make_option(c("-r", "--report_file"), type="character", default=NULL, help="report rmarkdown file", metavar="character")
 )
 
 opt_parser = OptionParser(option_list=option_list)
 opt = parse_args(opt_parser)
 
 wd=getwd()
 
-rmarkdown::render(opt$report_file, output_file = "Bcellmagic_report.html", knit_root_dir = wd, output_dir = wd,
-                    params = list(path_bibliography = opt$references,
-                                    path_css = opt$css,
-                                    path_logo = opt$logo))
+rmarkdown::render(opt$report_file, output_file = "Bcellmagic_report.html", knit_root_dir = wd, output_dir = wd)
diff --git a/modules/local/alakazam/alakazam_shazam_repertoires.nf b/modules/local/alakazam/alakazam_shazam_repertoires.nf
@@ -10,7 +10,7 @@ process ALAKAZAM_SHAZAM_REPERTOIRES {
     input:
     path(tab) // sequence tsv table in AIRR format
     path("Table_sequences.tsv")
-    tuple path(repertoire_report), path(references), path(css), path(logo)
+    tuple path(repertoire_report), path(css), path(logo)
 
     output:
     path("versions.yml"), emit: versions
@@ -19,7 +19,7 @@ process ALAKAZAM_SHAZAM_REPERTOIRES {
 
     script:
     """
-    execute_report.R --report_file ${repertoire_report} --references ${references}
+    execute_report.R --report_file ${repertoire_report}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/workflows/bcellmagic.nf b/workflows/bcellmagic.nf
@@ -131,7 +131,6 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi
 
 // Rmarkdown report file
 ch_rmarkdown_report = Channel.fromPath( ["$projectDir/assets/repertoire_comparison.Rmd",
-                                    "$projectDir/assets/references.bibtex",
                                     "$projectDir/assets/nf-core_style.css",
                                     "$projectDir/assets/nf-core-airrflow_logo_light.png"],
                                     checkIfExists: true).dump(tag: 'report files')