Merge pull request #344 from sanger-tol/tola406_genesetsyntenyyaml

Will's Update to MerquryFK

docs/usage.md

@@ -89,6 +89,8 @@ Now that's all downloaded we need to prep it. At this point it is all still gzip
 
 The below code will look through the current folder for files ending with `.fasta.gz` and decompresses it, it will then run our python script, `GA_data_prep.py`.
 
+NOTE: This will soon be superseeded by a rust tools `treeval_utils`, this will replace all of the accessory pythons scripts included in this document. Whilst also adding a program to verify your YAML.
+
 Command:
 
 ```bash
@@ -234,7 +236,7 @@ If your data isn't already in these formats, then let us know and we'll see how
 
 This command iterates through your bam files and converts them to fastq via samtools.
 
-```
+```bash
 cd { TO FOLDER OF BAM FILES }
 mkdir fastq
 for i in *bam
@@ -266,6 +268,7 @@ done
 This simply gzips (compresses) the fasta files.
 
 ```bash
+cd fasta
 for i in .fasta; do
   echo $i
   gzip $i

modules.json

@@ -79,7 +79,7 @@
                     },
                     "fastk/fastk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fastk/fastk/fastk-fastk.diff"
                     },