package requirement updated

README.md

@@ -6,6 +6,8 @@ NanoCaller is a computational method that integrates long reads in deep convolut
 NanoCaller is distributed under the [MIT License by Wang Genomics Lab](https://wglab.mit-license.org/).
 
 ## Latest Updates
+_**v3.4.2** (March 27 2024)_: CRAM files are supported in input as well as in phased output if whatshap version>=2 is being used with NanoCaller.
+
 _**v3.4.0** (July 31 2023)_: VCF files contain total and strand-specific allele depths for SNP calls from SNP calling models. A new mode for short ONT reads (5-10kbp) added. `--phase_qual_score` parameter filters out low quality SNP calls from phasing by WhatsHap; these SNP calls are kept in the output, but neither phased nor used for phasing reads.
 
 _**v3.3.0** (July 14 2023)_: Detailed description of SNP calls, including unfiltered SNP calls for variants determined to be false by NanoCaller, and inclusion of per-base probability output. Quality score has been adjusted to be on Phred scale.

environment.yml

@@ -12,8 +12,8 @@ dependencies:
   - python>=3.8
   - samtools>=1.10
   - tensorflow>=2.2
-  - whatshap>=1.0
+  - whatshap>=2.0
   - vcflib
   - intervaltree=3.*
   - tqdm
-  - rtg-tools
+  - rtg-tools