feat: add wrapper for rbt vcf_fix_iupac_alleles

bio/rbt/vcf_fix_iupac_alleles/environment.yaml

@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - rust-bio-tools =0.42.0
+  - bcftools =1.16
+  - snakemake-wrapper-utils =0.5.3

bio/rbt/vcf_fix_iupac_alleles/meta.yaml

@@ -0,0 +1,10 @@
+name: rbt vcf-fix-iupac-alleles
+description: |
+  Convert any IUPAC codes in alleles into Ns (in order to comply with VCF 4 specs).
+url: https://github.com/rust-bio/rust-bio-tools
+authors:
+  - Filipe G. Vieira
+input:
+  - VCF
+output:
+  - VCF/BCF

bio/rbt/vcf_fix_iupac_alleles/test/Snakefile

@@ -0,0 +1,16 @@
+
+rule vcf_fix_iupac_alleles:
+    input:
+        "{file}.vcf.gz",
+    output:
+        vcf="results/{file}.vcf.gz",
+        idx="results/{file}.vcf.gz.tbi",
+    log:
+        "logs/{file}.log",
+    params:
+        extra="",
+    threads: 1
+    resources:
+        mem_mb=1024,
+    wrapper:
+        "master/bio/rbt/vcf_fix_iupac_alleles"

bio/rbt/vcf_fix_iupac_alleles/wrapper.py

@@ -0,0 +1,21 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2023, Filipe G. Vieira"
+__license__ = "MIT"
+
+import tempfile
+from snakemake.shell import shell
+from snakemake_wrapper_utils.bcftools import get_bcftools_opts
+
+
+bcftools_opts = get_bcftools_opts(snakemake, parse_ref=False)
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+
+with tempfile.TemporaryDirectory() as tmpdir:
+    shell(
+        "(rbt vcf-fix-iupac-alleles {extra} < {snakemake.input[0]} | bcftools sort --temp-dir {tmpdir} {bcftools_opts}) {log}"
+    )
+
+    if snakemake.output.get("idx"):
+        shell("tabix -p vcf {snakemake.output.vcf}")

test.py

@@ -5192,13 +5192,21 @@ def test_verifybamid2():
     )
 
 @skip_if_not_modified
-def test_collapse_reads_to_fragments_bam():
+def test_rbt_collapse_reads_to_fragments_bam():
     run(
         "bio/rbt/collapse_reads_to_fragments-bam",
         ["snakemake", "--cores", "1", "--use-conda", "-F"],
     )
 
 
+@skip_if_not_modified
+def test_rbt_vcf_fix_iupac_alleles():
+    run(
+        "bio/rbt/vcf_fix_iupac_alleles",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "results/homo_sapiens-chrMT.vcf.gz"],
+    )
+
+
 @skip_if_not_modified
 def test_calc_consensus_reads():
     run(