containerization

README.md

@@ -22,20 +22,31 @@
 
 
 1. [**Build** meryl k-mer databases](#build-meryl-k-mer-databases)
-     - Requires: WGS sequencing libraries (Pacbio HiFi or Illumina PE short-insert `.fastq`'s)
-     - Output: (`.meryl`) k-mer database  
+<br>
+
+![](https://i.imgur.com/HK4ZMi2.png)
+
+- Requires: WGS sequencing libraries (Pacbio HiFi or Illumina PE short-insert `.fastq`'s)
+- Output: (`.meryl`) k-mer database  
+
+<br>
 
 
 2. [Assembly **Evaluation**](#assembly-evaluation)
-     - Requires: (`.meryl`) k-mer databases and corresponding genome assemblies (`.fasta`'s) you wish to evaluate. As well as HiC Libraries as optional input.
-     - Output:
-         - Assembly Stats (L#, N#, Scaffold, contig, etc.)
-         - BUSCO results
-         - QV Score
-         - K-mer Completeness
-         - genomescope profile
-         - Pretext Map (optional)
-         - **PDF Report aggregating all of the above**
+<br>
+
+![](https://i.imgur.com/8eLKPtK.png)
+
+- Requires: (`.meryl`) k-mer databases and corresponding genome assemblies (`.fasta`'s) you wish to evaluate. As well as HiC Libraries as optional input.
+- Output:
+    - Assembly Stats (L#, N#, Scaffold, contig, etc.)
+    - BUSCO results
+    - QV Score
+    - K-mer Completeness
+    - genomescope profile
+    - Pretext Map (optional)
+    - **PDF Report aggregating all of the above**
+
 
 ![](https://i.imgur.com/hWMo4PF.png)
 

installGEP.yaml

@@ -4,10 +4,7 @@ channels:
  - bioconda
  - anaconda
 dependencies:
- - snakemake==6.6.1
- - python>=3.9.10
- - tabulate=0.8.7
+ - snakemake==7.3.8
  - beautifulsoup4=4.9
- - mamba=0.15.2
- - pandoc=2.15.*
- - tectonic
+ - pandas
+ - numpy