Ignore OPERA-MS dir

.gitignore

@@ -1,3 +1,6 @@
+*.bt2
+OPERA-MS/
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

sbx_demic_ref.smk

@@ -12,13 +12,23 @@ DEMIC_FP = MAPPING_FP / "demic"
 DEMIC_REF_FP = DEMIC_FP / "ref"
 
 
+def get_demic_path() -> Path:
+    for fp in sys.path:
+        if fp.split("/")[-1] == "sbx_demic":
+            return Path(fp)
+    raise Error(
+        "Filepath for demic not found, are you sure it's installed under extensions/sbx_demic?"
+    )
+
+
 localrules:
     all_demic_ref,
 
 
 rule all_demic_ref:
     input:
-        DEMIC_REF_FP / "all_PTR.txt"
+        #DEMIC_REF_FP / "all_PTR.txt"
+        expand(DEMIC_REF_FP / "OPERA_MS" / "{sample}" / "contigs.fasta", sample=Samples.keys())
 
 
 rule install_opera_ms:
@@ -40,9 +50,20 @@ rule install_opera_ms:
 rule run_opera_ms:
     input:
         DEMIC_REF_FP / ".installed",
-        reads=QC_FP / "decontam" / "{sample}_{rp}.fastq.gz",
+        reads=expand(QC_FP / "decontam" / "{{sample}}_{rp}.fastq.gz", rp=Pairs),
         contigs=Cfg["sbx_demic"]["ref_fp"],
-
+    output:
+        DEMIC_REF_FP / "OPERA_MS" / "{sample}" / "contigs.fasta",
+    params:
+        demic_fp=str(get_demic_path()),
+        threads=Cfg["sbx_demic"]["demic_threads"],
+    conda:
+        "envs/demic_ref_env.yml"
+    shell:
+        """
+        cd {params.demic_fp}/OPERA-MS
+        perl OPERA-MS.pl --num-processors {params.threads} --long-read {input.contigs} --short-read1 {input.reads[0]} --short-read2 {input.reads[1]} --out-dir {output} --no-polishing
+        """
 
 
 
@@ -53,12 +74,12 @@ rule run_opera_ms:
 rule run_pycov3_ref:
     input:
         DEMIC_FP / "sorted",
-        COASSEMBLY_DEMIC_FP / "max_bin" / "max_bin",
+        #COASSEMBLY_DEMIC_FP / "max_bin" / "max_bin",
     output:
         directory(DEMIC_FP / "pycov3"),
     params:
         sam_dir=str(DEMIC_FP / "sorted"),
-        fasta_dir=str(COASSEMBLY_DEMIC_FP / "max_bin"),
+        #fasta_dir=str(COASSEMBLY_DEMIC_FP / "max_bin"),
         extras=Cfg["sbx_demic"]["extras"],
     threads: Cfg["sbx_demic"]["demic_threads"]
     resources:
@@ -68,6 +89,8 @@ rule run_pycov3_ref:
         "envs/demic_bio_env.yml"
     log:
         LOG_FP / "run_pycov3.log",
+    benchmark:
+        BENCHMARK_FP / "run_pycov3_ref.txt",
     shell:
         """
         pycov3 -S {params.sam_dir} -F {params.fasta_dir} -O {output} -X {params.extras} 2>&1 | tee {log}