perf: autobump bio/snpeff/annotate (#1038)

Automatic update of bio/snpeff/annotate.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/snpeff/annotate/environment.yaml

@@ -3,6 +3,6 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - snpeff ==4.3.1t
-  - bcftools =1.11
-  - snakemake-wrapper-utils ==0.1.3
+  - snpeff =5.1
+  - bcftools =1.16
+  - snakemake-wrapper-utils =0.5.2

bio/snpeff/annotate/meta.yaml

@@ -1,4 +1,16 @@
 name: "snpeff"
-description: Annotate predicted effect of nucleotide changes with `SnpEff <https://pcingola.github.io/SnpEff/se_introduction/>`_
+description: Annotate predicted effect of nucleotide changes with SnpEff.
+url: https://pcingola.github.io/SnpEff/se_introduction/
 authors:
   - Bradford Powell
+input:
+  - calls: input VCF/BCF file
+  - db: SnpEff database
+output:
+  - calls: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
+  - genes: genes output file (optional)
+  - stats: stats file (optional)
+  - csvstats: stats CSV file (optional)
+params:
+  - java_opts: additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
+  - extra: additional program arguments.

bio/snpeff/annotate/test/Snakefile

@@ -8,11 +8,25 @@ rule snpeff:
         csvstats="snpeff/{sample}.csv" # summary statistics in CSV, optional
     log:
         "logs/snpeff/{sample}.log"
-    # optional specification of memory usage of the JVM that snakemake will respect with global
-    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
-    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
-    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
     resources:
+        java_opts="-XX:ParallelGCThreads=10",
         mem_mb=4096
     wrapper:
         "master/bio/snpeff/annotate"
+
+rule snpeff_nostats:
+    input:
+        calls="{sample}.vcf",
+        db="resources/snpeff/ebola_zaire"
+    output:
+        calls="snpeff_nostats/{sample}.vcf",    # the main output file
+        # if either "genes" or "stats" outputs are provided, both are created
+    log:
+        "logs/snpeff_nostats/{sample}.log"
+    params:
+        java_opts="-XX:ParallelGCThreads=10",
+        extra=""                 # optional parameters
+    resources:
+        mem_mb=1024
+    wrapper:
+        "master/bio/snpeff/annotate"

test.py

@@ -3231,7 +3231,7 @@ def test_star_index():
 def test_snpeff_annotate():
     run(
         "bio/snpeff/annotate",
-        ["snakemake", "--cores", "1", "snpeff/fake_KJ660346.vcf", "--use-conda", "-F"],
+        ["snakemake", "--cores", "1", "snpeff/fake_KJ660346.vcf", "snpeff_nostats/fake_KJ660346.vcf", "--use-conda", "-F"],
     )
 
 
@@ -3250,23 +3250,6 @@ def test_snpeff_download():
     )
 
 
-@skip_if_not_modified
-def test_snpeff_nostats():
-    run(
-        "bio/snpeff/annotate",
-        [
-            "snakemake",
-            "--cores",
-            "1",
-            "snpeff_nostats/fake_KJ660346.vcf",
-            "--use-conda",
-            "-F",
-            "-s",
-            "Snakefile_nostats",
-        ],
-    )
-
-
 @skip_if_not_modified
 def test_strelka_germline():
     run(