diff --git a/bio/ngsbits/sampleancestry/environment.linux-64.pin.txt b/bio/ngsbits/sampleancestry/environment.linux-64.pin.txt new file mode 100644 index 00000000000..9e396b084a8 --- /dev/null +++ b/bio/ngsbits/sampleancestry/environment.linux-64.pin.txt @@ -0,0 +1,166 @@ +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +# created-by: conda 24.9.2 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.8.30-hbcca054_0.conda#c27d1c142233b5bc9ca570c6e2e0c244 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45 +https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6 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b/bio/ngsbits/sampleancestry/meta.yaml new file mode 100644 index 00000000000..bd70b883cdc --- /dev/null +++ b/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. diff --git a/bio/ngsbits/sampleancestry/test/Snakefile b/bio/ngsbits/sampleancestry/test/Snakefile new file mode 100644 index 00000000000..5b15bd9a07c --- /dev/null +++ b/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" diff --git a/bio/ngsbits/sampleancestry/test/sample.vcf b/bio/ngsbits/sampleancestry/test/sample.vcf new file mode 100644 index 00000000000..16a571c2c56 --- /dev/null +++ b/bio/ngsbits/sampleancestry/test/sample.vcf @@ -0,0 +1,11 @@ +##fileformat=VCFv4.0 +##INFO= +##INFO= +##INFO= +##INFO= +#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 diff --git a/bio/ngsbits/sampleancestry/wrapper.py b/bio/ngsbits/sampleancestry/wrapper.py new file mode 100644 index 00000000000..5d6a1161f21 --- /dev/null +++ b/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}" +) diff --git a/test_wrappers.py b/test_wrappers.py index 5c47f4ea9b8..cee5580e7d4 100644 --- a/test_wrappers.py +++ b/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",