feat: NGS-bits SampleAncestry

bio/ngsbits/sampleancestry/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ngs-bits=2024_11

bio/ngsbits/sampleancestry/meta.yaml

@@ -0,0 +1,13 @@
+name: NGS-bits SampleAncestry
+url: https://github.com/imgag/ngs-bits/blob/master/doc/tools/SampleAncestry/index.md
+description: Estimates the ancestry of a sample based on variants.
+authors:
+  - Thibault Dayris
+input:
+  - Path to one or multiple VCF file(s).
+output:
+  - Path to results table (TSV)
+params:
+  - extra: Optional parameters besides IO
+notes: |
+  To estimate ancestry, the input VCF file must have enough variants AND variants that overlaps known human variants ancestry.

bio/ngsbits/sampleancestry/test/Snakefile

@@ -0,0 +1,13 @@
+rule test_ngsbits_sampleancestry:
+    input:
+        # Either a single VCF or a list of VCF files
+        "sample.vcf",
+    output:
+        "ancestry.tsv",
+    threads: 1
+    log:
+        "ancestry.log",
+    params:
+        extra="-min_snps 4 -build hg19",
+    wrapper:
+        "master/bio/ngsbits/sampleancestry"

bio/ngsbits/sampleancestry/test/sample.vcf

@@ -0,0 +1,11 @@
+##fileformat=VCFv4.0
+##INFO=<ID=AF_AFR,Number=1,Type=String,Description="no description available">
+##INFO=<ID=AF_EAS,Number=1,Type=String,Description="no description available">
+##INFO=<ID=AF_EUR,Number=1,Type=String,Description="no description available">
+##INFO=<ID=AF_SAS,Number=1,Type=String,Description="no description available">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
+chr1	69270	.	A	G	.	.	AF_AFR=0.360;AF_EAS=0.998;AF_EUR=0.911;AF_SAS=0.902	GT	1/1
+chr1	69897	.	T	C	.	.	AF_AFR=0.312;AF_EAS=0.777;AF_EUR=0.844;AF_SAS=0.805	GT	0/1
+chr1	325155	.	C	A	.	.	AF_AFR=0.653;AF_EAS=0.971;AF_EUR=0.769;AF_SAS=0.497	GT	1/1
+chr1	881627	.	G	A	.	.	AF_AFR=0.130;AF_EAS=0.658;AF_EUR=0.636;AF_SAS=0.565	GT	0/1
+chr1	914852	.	G	C	.	.	AF_AFR=0.249;AF_EAS=0.722;AF_EUR=0.596;AF_SAS=0.622	GT	1/1

bio/ngsbits/sampleancestry/wrapper.py

@@ -0,0 +1,23 @@
+# coding: utf-8
+
+"""Snakemake wrapper for NGS-bits SampleAncestry"""
+
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2024, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(
+    stdout=False,
+    stderr=True,
+)
+extra = snakemake.params.get("extra", "")
+
+shell(
+    "SampleAncestry {extra}"
+    " -in {snakemake.input}"
+    " -out {snakemake.output:q}"
+    " {log}"
+)

test_wrappers.py

@@ -3579,6 +3579,20 @@ def test_nanosim_metagenome(run):
     )
 
 
+def test_ngsbits_sampleancestry(run):
+    run(
+        "bio/ngsbits/sampleancestry",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "ancestry.tsv",
+        ],
+    )
+
+
 def test_ngsderive(run):
     run(
         "bio/ngsderive",
@@ -5959,12 +5973,14 @@ def test_vg_autoindex_giraffe(run):
         ["snakemake", "--cores", "1", "resources/genome.dist", "--use-conda", "-F"],
     )
 
+
 def test_vg_autoindex_map(run):
     run(
         "bio/vg/autoindex",
         ["snakemake", "--cores", "1", "resources/genome.xg", "--use-conda", "-F"],
     )
 
+
 def test_vg_construct(run):
     run(
         "bio/vg/construct",