feat: added wrapper for bcftools stats (#201)

* added wrapper for bcftools stats

* added test case, updated bcftools version

* formatted wrapper with black

* added bcftools stats test case

* updated test output, added log

* corrected name of input in bcftools_stats test wrapper

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>

bio/bcftools/stats/environment.yaml

@@ -0,0 +1,5 @@
+channels:
+  - bioconda
+  - conda-forge
+dependencies:
+  - bcftools ==1.12

bio/bcftools/stats/meta.yaml

@@ -0,0 +1,9 @@
+name: bcftools stats
+description: Generate VCF stats using bcftools stats.
+url: https://github.com/samtools/bcftools
+authors:
+  - William Rowell
+input:
+  - BCF, VCF, or VCF.gz input
+output:
+  - stats text file

bio/bcftools/stats/test/Snakefile

@@ -0,0 +1,11 @@
+rule bcf_stats:
+    input:
+        "{prefix}"
+    output:
+        "{prefix}.stats.txt"
+    log:
+        "{prefix}.bcftools.stats.log"
+    params:
+        ""
+    wrapper:
+        "master/bio/bcftools/stats"

bio/bcftools/stats/wrapper.py

@@ -0,0 +1,18 @@
+__author__ = "William Rowell"
+__copyright__ = "Copyright 2020, William Rowell"
+__email__ = "wrowell@pacb.com"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+# bcftools takes additional decompression threads through --threads
+# Other threads are *additional* threads passed to the '--threads' argument
+threads = (
+    "" if snakemake.threads <= 1 else " --threads {} ".format(snakemake.threads - 1)
+)
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
+shell(
+    "bcftools stats {threads} {snakemake.params} {snakemake.input} > {snakemake.output} {log}"
+)

test.py

@@ -781,10 +781,10 @@ def test_bcftools_reheader():
 
 
 @skip_if_not_modified
-def test_bcftools_reheader():
+def test_bcftools_stats():
     run(
-        "bio/bcftools/reheader",
-        ["snakemake", "--cores", "1", "a.reheader.bcf", "--use-conda", "-F"],
+        "bio/bcftools/stats",
+        ["snakemake", "--cores", "1", "a.bcf.stats.txt", "--use-conda", "-F"],
     )