fix expected suffixarray path; fix #1334

snakemake · Oct 21, 2024 · be05337 · be05337
1 parent 8fec54f
commit be05337
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Showing 3 changed files with 10 additions and 3 deletions.
diff --git a/bio/bwa-meme/index/wrapper.py b/bio/bwa-meme/index/wrapper.py
@@ -45,7 +45,7 @@ def get_valid_suffix(path):
     raise ValueError("Output files must share common prefix up to their file endings.")
 (prefix,) = prefixes
 
-suffixarray = snakemake.input[0] + ".suffixarray_uint64"
+suffixarray = f"{prefix}.suffixarray_uint64"
 dirname = path.dirname(suffixarray)
 basename = path.basename(suffixarray)
 num_models = snakemake.params.get("num_models", 268435456)  # change only for testing!

diff --git a/bio/bwa-memx/index/meta.yaml b/bio/bwa-memx/index/meta.yaml
@@ -2,4 +2,11 @@ name: "bwa-mem2 index"
 description: "Creates a bwa-mem, bwa-mem2 or bwa-meme index."
 authors:
   - Christopher Schröder
-  - Patrik Smeds
+  - Patrik Smeds
+input:
+  - fasta file
+output:
+  - BWA index files, which should all share a common prefix. Note that this prefix can include an output directory path, for example "myindex/prefix".
+params:
+  - bwa: 'the type of BWA index you want to build: "bwa-mem", "bwa-mem2", "bwa-meme"'
+  - num_models: 'for BWA-MEME, the number of models for the P-RMI training step (default: 268435456)'
diff --git a/bio/bwa-memx/index/wrapper.py b/bio/bwa-memx/index/wrapper.py
@@ -74,7 +74,7 @@ def get_valid_suffix(path):
     raise ValueError("Output files must share common prefix up to their file endings.")
 (prefix,) = prefixes
 
-suffixarray = snakemake.input[0] + ".suffixarray_uint64"
+suffixarray = f"{prefix}.suffixarray_uint64"
 dirname = path.dirname(suffixarray)
 basename = path.basename(suffixarray)
 num_models = snakemake.params.get("num_models", 268435456)  # change only for testing!