feat: added RGI for AMR detection + bug fix

[m-jahn]

No description provided.

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Language	Validation result
SNAKEMAKE_SNAKEFMT	Fail ❌
YAML_PRETTIER	Pass ✅

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SNAKEMAKE_SNAKEFMT

=====> Diff for /github/workspace/workflow/rules/common.smk <=====

--- original
+++ new
@@ -55,7 +55,7 @@
             "results/annotation/{tool}/{sample}/{sample}.{ext}",
             tool=tool,
             sample=samples.index,
-            ext=["gff", "fna"]
+            ext=["gff", "fna"],
         )
     inputs += expand(
         "results/qc/quast/report.txt",
@@ -71,9 +71,7 @@
         )
     if not config["rgi"]["skip"]:
         inputs += expand(
-            "results/qc/rgi/{sample}.{ext}",
-            sample=samples.index,
-            ext=["txt", "json"]
+            "results/qc/rgi/{sample}.{ext}", sample=samples.index, ext=["txt", "json"]
         )
     return inputs
 [INFO] 1 file(s) would be changed 😬
[INFO] 1 file(s) would be left unchanged 🎉

[github-actions]

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Language	Validation result
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML_PRETTIER	Pass ✅

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[github-actions]

Super-linter summary

Language	Validation result
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML_PRETTIER	Pass ✅

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[rabioinf]

looks good.