some chenges

bio-informatician · Aug 1, 2023 · 4417482 · 4417482
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commit 4417482
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diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -0,0 +1,5 @@
+{
+    "recommendations": [
+        "snakemake.snakemake-lang"
+    ]
+}
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -2,3 +2,20 @@
 # Please follow the best practices: 
 # https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html,
 # in particular regarding the standardized folder structure mentioned there. 
+
+FASTA_PREFIXES = [
+    "GCA_0090
+]
+
+rule all:
+    input:
+        expand(
+            [   "results/annotate/{fasta_prefix}/{fasta_prefix}_proteins.faa",
+                "results/annotate/{fasta_prefix}/{fasta_prefix}_mmseq2.tsv",
+                "results/annotate/{fasta_prefix}/{fasta_prefix}_genes.tsv",
+                "results/annotate/{fasta_prefix}/{fasta_prefix}_taxonomy.tsv",
+                directory("results/annotate/{fasta_prefix}/mmseq2"),
+            ],
+            fasta_prefix = FASTA_PREFIXES
+        )   
+