Add citation

.github/workflows/r.yml

@@ -30,7 +30,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
-    steps:
+    steps:hbgvn
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2

CITATION.cff

@@ -29,5 +29,5 @@ keywords:
   - Epistasis
   - Gene Interactions
 license: GPL-3.0-or-later
-version: v1.4
+version: v1.5
 date-released: '2024-01-04'

README.md

@@ -94,7 +94,7 @@ num_clusts_CDS = 2, SnpEff_Annotate = F, snp_filt_method = snp_filt_method)
 
 ## Citation
 
-Please cite LDWeaver using: Mallawaarachchi, Sudaraka et al. Detecting co-selection through excess linkage disequilibrium in bacterial genomes. bioRxiv 2023.08.04.551407; doi: https://doi.org/10.1101/2023.08.04.551407
+Please cite LDWeaver using: Mallawaarachchi, S. et al. Detecting co-selection through excess linkage disequilibrium in bacterial genomes, NAR Genomics and Bioinformatics, Volume 6, Issue 2, June 2024, lqae061, https://doi.org/10.1093/nargab/lqae061
 
 ## Detailed Workthrough using Real Data
 
@@ -103,7 +103,7 @@ LDWeaver. The alignment with 616 *S. pnuemoniae* genomes is available
 <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EeLNWOGYDi5Bk4PVY6JZF10BEDM2ckSCMq4nZqX8OGimJg?e=3AfBhf" target="_blank">here</a>, and 
 the same sample.gbk annotation was used to generate this alignment (also available <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_011900.1?report=gbwithparts&log$=seqview" target="_blank">here</a>).
 
-> **Note:** Alternatively, since LDWeaver v1.2, you can download and use the <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EdQdnfYv3KRBiuYW73BEGXgBbtZR2SSdty_qiNgjJflp5w?e=vbpeEp" target="_blank">SNP-only alignment</a> with the accompanying <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EZoekLiIyZZKuVAoHoWob1cBk2yBSOfr4MeuLp_VgKJG5g" target="_blank">positions</a> file to generate the same results.
+> **Note:** Alternatively, you can download and use the <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EdQdnfYv3KRBiuYW73BEGXgBbtZR2SSdty_qiNgjJflp5w?e=vbpeEp" target="_blank">SNP-only alignment</a> with the accompanying <a href="https://uio-my.sharepoint.com/:u:/g/personal/sudarakm_uio_no/EZoekLiIyZZKuVAoHoWob1cBk2yBSOfr4MeuLp_VgKJG5g" target="_blank">positions</a> file to generate the same results.
 
 For this example, it is assumed that the current working directory is set to 
 `~/LDWeaver_run` and the
@@ -344,4 +344,4 @@ separated format
 5. Temp/X_annotated_stats.html - annotations and statistics in html
 format
 6. Temp/X_snps.vcf, Temp/X_snps_ann.vcf - input and output from the snpEff
-annotation pipeline
+annotation pipeline