Updated Docs

CHANGELOG.md

@@ -40,11 +40,18 @@ This builds on the initial release by adding subworkflows which generate kmer ba
 - Fix a bug in build_alignment_blocks.py to avoid indexing errors happening in large genomes.
 - Change output BEDGRAPH from EXTRACT_TELO module.
 
+#### Hot Fix 1
+- Adding support for multi-library cram input.
+
+#### Hot Fix 2
+- Adding support to select subworkflows to use in pipeline run.
+
 ### Parameters
 
 | Old Parameter | New Parameter |
 | ------------- | ------------- |
 | -             | --juicer      |
+| -             | --steps       |
 
 ### Software dependencies
 

CITATIONS.md

@@ -34,6 +34,10 @@
 
   > Durand, N.C. et al. 2016. ‘Juicer provides a one-click system for analyzing loop-resolution hi-C experiments’, Cell Systems, 3(1), pp. 95–98. doi:10.1016/j.cels.2016.07.002.
 
+- [Merqury_FK](https://github.com/thegenemyers/MERQURY.FK)
+
+  > Myers, G., Rhie, A. (2024). MerquryFK & KatFK. [online]. https://github.com/thegenemyers/MERQURY.FK. (Accessed on 20 September 2024).
+
 - [Minimap2](https://pubmed.ncbi.nlm.nih.gov/34623391/)
 
   > Li, H. 2021. ‘New strategies to improve MINIMAP2 alignment accuracy’, Bioinformatics, 37(23), pp. 4572–4574. doi:10.1093/bioinformatics/btab705.
@@ -72,7 +76,7 @@
 
 - [Samtools](https://pubmed.ncbi.nlm.nih.gov/33590861/)
 
-  > Di Tommaso, Paolo, et al. 2017. “Nextflow Enables Reproducible Computational Workflows.” Nature Biotechnology, 35(4), pp. 316–19, https://doi.org/10.1038/nbt.3820.
+  > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Feb 16;10(2):giab008. doi: 10.1093/gigascience/giab008. PMID: 33590861; PMCID: PMC7931819.
 
 - [SeqTK](https://github.com/lh3/seqtk)