fix: log file handling and other small improvements for bcftools wrap…

…pers (#429)

* Added logs to several bcftools modules

* Added bcftools_opts to norm

* Added snakemake-wrapper-utils

* Added params extra, to be consistent with other modules

* Disabled parsing of memory and temp_dir

* Formatting with snakefmt

* Added test

* Fixed typo

* Added missing extra param

bio/bcftools/call/wrapper.py

@@ -6,6 +6,8 @@
 
 from snakemake.shell import shell
 
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 
 class CallerOptionError(Exception):
     pass
@@ -24,5 +26,6 @@ class CallerOptionError(Exception):
 
 shell(
     "bcftools call {options} {caller_opt} --threads {snakemake.threads} "
-    "-o {snakemake.output.calls} {snakemake.input.pileup} 2> {snakemake.log}"
+    "-o {snakemake.output.calls} {snakemake.input.pileup} "
+    "{log}"
 )

bio/bcftools/index/wrapper.py

@@ -6,7 +6,9 @@
 
 from snakemake.shell import shell
 
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 ## Extract arguments
 extra = snakemake.params.get("extra", "")
 
-shell("bcftools index" " {extra}" " {snakemake.input[0]}")
+shell("bcftools index {extra} {snakemake.input[0]} {log}")

bio/bcftools/merge/wrapper.py

@@ -6,7 +6,10 @@
 
 from snakemake.shell import shell
 
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 shell(
     "bcftools merge {snakemake.params} -o {snakemake.output[0]} "
-    "{snakemake.input.calls}"
+    "{snakemake.input.calls} "
+    "{log}"
 )

bio/bcftools/mpileup/wrapper.py

@@ -6,6 +6,8 @@
 
 from snakemake.shell import shell
 
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
 
 class MissingReferenceError(Exception):
     pass
@@ -26,5 +28,6 @@ class MissingReferenceError(Exception):
 shell(
     "bcftools mpileup {options} --threads {snakemake.threads} "
     "--output {snakemake.output.pileup} "
-    "{snakemake.input.alignments} 2> {snakemake.log}"
+    "{snakemake.input.alignments} "
+    "{log}"
 )

bio/bcftools/norm/environment.yaml

@@ -2,4 +2,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - bcftools =1.11
+  - bcftools =1.11
+  - snakemake-wrapper-utils =0.2

bio/bcftools/norm/meta.yaml

@@ -2,3 +2,4 @@ name: bcftools norm
 description: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows. For more information see `BCFtools documentation <https://www.htslib.org/doc/bcftools.html#norm>`_.
 authors:
   - Dayne Filer
+  - Filipe G. Vieira

bio/bcftools/norm/test/Snakefile

@@ -1,9 +1,11 @@
 rule norm_vcf:
     input:
-        "{prefix}.vcf"
+        "{prefix}.bcf",
     output:
-        "{prefix}.vcf"
+        "{prefix}.norm.vcf",
+    log:
+        "{prefix}.norm.log",
     params:
-        ""  # optional parameters for bcftools norm (except -o)
+        extra="--rm-dup none",  # optional
     wrapper:
         "master/bio/bcftools/norm"

bio/bcftools/norm/wrapper.py

@@ -5,8 +5,13 @@
 
 
 from snakemake.shell import shell
+from snakemake_wrapper_utils.bcftools import get_bcftools_opts
+
+bcftools_opts = get_bcftools_opts(snakemake, parse_memory=False, parse_temp_dir=False)
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 
 shell(
-    "bcftools norm {snakemake.params} {snakemake.input[0]} " "-o {snakemake.output[0]}"
+    "bcftools norm {bcftools_opts} {extra} {snakemake.input[0]} -o {snakemake.output[0]} {log}"
 )

bio/bcftools/reheader/wrapper.py

@@ -6,6 +6,8 @@
 
 from snakemake.shell import shell
 
+log = snakemake.log_fmt_shell(stdout=False, stderr=True)
+
 ## Extract arguments
 header = snakemake.input.get("header", "")
 if header:
@@ -30,5 +32,6 @@
     "{snakemake.input.vcf} "
     "| bcftools view "
     "{view_extra} "
-    "> {snakemake.output}"
+    "> {snakemake.output} "
+    "{log}"
 )

test.py

@@ -773,10 +773,18 @@ def test_bcftools_reheader():
 
 
 @skip_if_not_modified
-def test_bcftools_view_sample_vcf():
+def test_bcftools_reheader():
     run(
-        "bio/bcftools/view",
-        ["snakemake", "--cores", "1", "a.view_sample.vcf", "--use-conda", "-F"],
+        "bio/bcftools/reheader",
+        ["snakemake", "--cores", "1", "a.reheader.bcf", "--use-conda", "-F"],
+    )
+
+
+@skip_if_not_modified
+def test_bcftools_norm():
+    run(
+        "bio/bcftools/norm",
+        ["snakemake", "--cores", "1", "a.norm.vcf", "--use-conda", "-F"],
     )