Merge pull request #3 from RIVM-bioinformatics/fix_envs

deps: split deps over two envs

src/skiml_cluster/workflow/Snakefile

@@ -78,7 +78,7 @@ rule make_tree:
     output:
         OUTPUT_DIR + "/tree.nwk",
     conda:
-        "envs/main.yaml"
+        "envs/vk.yaml"
     shell:
         """
         vk phylo tree upgma {input} > {output}
@@ -91,7 +91,7 @@ rule make_aln:
     output:
         OUTPUT_DIR + "/vcf_snp.aln.fasta",
     conda:
-        "envs/main.yaml"
+        "envs/vk.yaml"
     shell:
         """
         vk phylo fasta {input} > {output}

src/skiml_cluster/workflow/envs/main.yaml

@@ -1,9 +1,9 @@
 channels:
 - bioconda
 - conda-forge
+- nodefaults
 dependencies:
-- vcfkit==0.2.9
 - snp-dists==0.8.2
 - vcftools==0.1.16
 - python>=3.7
-- muscle<5.1
+- samtools

src/skiml_cluster/workflow/envs/vk.yaml

@@ -0,0 +1,7 @@
+channels:
+- bioconda
+- conda-forge
+- nodefaults
+dependencies:
+- vcfkit==0.2.9
+- muscle<5.1