Snpsites (#480)

* output constant sites as a val as well as a file so it can be passed into iqtree

* Using an env variable because that's far safer!

* Update software/snpsites/main.nf

* remove hardcoded param that should be a user option

* Update software/snpsites/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

software/snpsites/main.nf

@@ -29,8 +29,9 @@ process SNPSITES {
     script:
     def software = getSoftwareName(task.process)
     """
-    snp-sites -c \\
+    snp-sites \\
         $alignment \\
+        $options.args \\
         > filtered_alignment.fas
 
     echo \$(snp-sites -C $alignment) > constant.sites.txt

tests/software/snpsites/test.yml

@@ -4,6 +4,6 @@
     - snpsites
   files:
     - path: output/snpsites/filtered_alignment.fas
-      md5sum: 34a3d2ae4439447eabe80282f4625dba
+      md5sum: f96c7513003e878e16fa9eac9fcda0f4
     - path: output/snpsites/constant.sites.txt
       md5sum: 8b9b226e3787f7baaefce07405af22c9