fix: manage properly bwamem2 indexes

jlanga · Apr 26, 2024 · 6f585f0 · 6f585f0
1 parent 4c74cb9
commit 6f585f0
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Showing 2 changed files with 23 additions and 11 deletions.
diff --git a/workflow/rules/preprocess/index.smk b/workflow/rules/preprocess/index.smk
@@ -3,20 +3,24 @@ rule preprocess__index:
     input:
         fa=REFERENCE / f"{REFERENCE_NAME}.fa.gz",
     output:
-        mock=touch(PRE_INDEX / f"{REFERENCE_NAME}"),
-        buckets=[
-            PRE_INDEX / f"{reference_name}.{suffix}"
-            for reference_name in [REFERENCE_NAME]
-            for suffix in "0123 amb ann bwt.2bit.64 pac".split()
-        ],
+        buckets=multiext(
+            str(PRE_INDEX / f"{REFERENCE_NAME}."),
+            "0123",
+            "amb",
+            "ann",
+            "bwt.2bit.64",
+            "pac",
+        ),
     log:
         PRE_INDEX / f"{REFERENCE_NAME}.log",
     conda:
         "__environment__.yml"
+    params:
+        prefix=PRE_INDEX / f"{REFERENCE_NAME}",
     shell:
         """
         bwa-mem2 index \
-            -p {output.mock} \
+            -p {params.prefix} \
             {input.fa} \
         > {log} 2>&1
         """
diff --git a/workflow/rules/preprocess/map.smk b/workflow/rules/preprocess/map.smk
@@ -3,24 +3,32 @@ rule preprocess__map__bwamem2__:
     input:
         forward_=READS / "{population}.{library}_1.fq.gz",
         reverse_=READS / "{population}.{library}_2.fq.gz",
-        index=PRE_INDEX / f"{REFERENCE_NAME}",
+        buckets=multiext(
+            str(PRE_INDEX / f"{REFERENCE_NAME}."),
+            "0123",
+            "amb",
+            "ann",
+            "bwt.2bit.64",
+            "pac",
+        ),
         reference=REFERENCE / f"{REFERENCE_NAME}.fa.gz",
     output:
         cram=PRE_MAP / "{population}.{library}.cram",
-    params:
-        rg_tag=compose_rg_tag,
     threads: 24
     log:
         PRE_MAP / "{population}.{library}.bwa_mem.log",
     conda:
         "__environment__.yml"
+    params:
+        rg_tag=compose_rg_tag,
+        prefix=PRE_INDEX / f"{REFERENCE_NAME}",
     shell:
         """
         ( bwa-mem2 mem \
             -M \
             -R '{params.rg_tag}' \
             -t {threads} \
-            {input.index} \
+            {params.prefix} \
             {input.forward_} \
             {input.reverse_} \
         | samtools sort \