feat: NGS-bits SampleSimilarity

bio/ngsbits/samplesimilarity/environment.linux-64.pin.txt

@@ -0,0 +1,122 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+# created-by: conda 24.9.2
+@EXPLICIT
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bio/ngsbits/samplesimilarity/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ngs-bits=2022_12

bio/ngsbits/samplesimilarity/meta.yaml

@@ -0,0 +1,12 @@
+name: NGS-bits SampleSimilarity
+url: https://github.com/imgag/ngs-bits/blob/master/doc/tools/SampleSimilarity/index.md
+authors:
+  - Thibault Dayris
+input:
+  - samples: list of paths to vcf/vcf.gz files, or list of paths to bam/sam/cram files
+  - ref: Optional path to reference genome index file (FAI). Required for CRAM input.
+  - roi: Optional path to regions of interest (BED).
+output:
+  - Path to output TSV results
+params:
+  - extra: Optional parameters besides IO, or `-mode`.

bio/ngsbits/samplesimilarity/test/Snakefile

@@ -0,0 +1,14 @@
+rule test_ngsbits_samplesimilarity:
+    input:
+        # ref="", # Optional path to fasta.fai file
+        # roi="", # Optional path to regions of interest (bed)
+        samples=expand("{sample}.vcf", sample=("a", "b")),
+    output:
+        "similarity.tsv",
+    threads: 1
+    log:
+        "samplesimilarity.log",
+    params:
+        extra="-build hg19",
+    wrapper:
+        "master/bio/ngsbits/samplesimilarity"

bio/ngsbits/samplesimilarity/test/a.vcf

@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##fileDate=20170110
+##source=pindel
+##reference=hg38
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##FORMAT=<ID=PL,Number=3,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
+7	140434574	.	C	CAAAAAAAGCAAAGTAAAAAGAAGAAAAAAACAACA	.	PASS	END=140434574;HOMLEN=5;HOMSEQ=AAAAA;SVLEN=35;SVTYPE=INS	GT:AD	0/0:317,6
+1	55238227	.	CCTGCCACTGAGCCTCATGCCTTCACGTGTCTGTTCCCCCCGCTTTTCCTTT	T	.	PASS	END=55238278;HOMLEN=7;HOMSEQ=CTGCCAC;SVLEN=-51;SVTYPE=DEL	GT:AD	0/0:40789,1734

bio/ngsbits/samplesimilarity/test/b.vcf

@@ -0,0 +1,18 @@
+##fileformat=VCFv4.0
+##fileDate=20170110
+##source=pindel
+##reference=hg38
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=HOMLEN,Number=1,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=PF,Number=1,Type=Integer,Description="The number of samples carry the variant">
+##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
+##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
+##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
+##INFO=<ID=NTLEN,Number=.,Type=Integer,Description="Number of bases inserted in place of deleted code">
+##FORMAT=<ID=PL,Number=3,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Reference depth, how many reads support the reference">
+##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Allele depth, how many reads support this allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
+7	140434574	.	C	CAAAAAAAGCAAAGTAAAAAGAAGAAAAAAACAACA	.	PASS	END=140434574;HOMLEN=5;HOMSEQ=AAAAA;SVLEN=35;SVTYPE=INS	GT:AD	0/0:317,6
+1	55238227	.	CCTGCCACTGAGCCTCATGCCTTCACGTGTCTGTTCCCCCCGCTTTTCCTTT	C	.	PASS	END=55238278;HOMLEN=7;HOMSEQ=CTGCCAC;SVLEN=-51;SVTYPE=DEL	GT:AD	0/0:40789,1734

bio/ngsbits/samplesimilarity/wrapper.py

@@ -0,0 +1,38 @@
+# coding: utf-8
+
+"""Snakemake wrapper for NGS-bits SampleSimilarity"""
+
+__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=True,
+    stderr=True,
+)
+extra = snakemake.params.get("extra", "")
+ref = snakemake.input.get("ref")
+if ref:
+    extra += f" -ref '{ref}' "
+
+roi = snakemake.input.get("roi")
+if roi:
+    extra += f" -roi '{roi}' "
+
+input_files = snakemake.input.get("samples")
+if all(str(i).endswith(("vcf", "vcf.gz")) for i in input_files):
+    extra += " -mode vcf "
+elif all(str(i).endswith(("sam", "bam", "cram")) for i in input_files):
+    extra += " -mode bam "
+else:
+    extra += " -mode gsvar "
+
+shell(
+    "SampleSimilarity {extra} "
+    "-in {input_files} "
+    "-out '{snakemake.output}' "
+    "{log}"
+)

test_wrappers.py

@@ -196,6 +196,21 @@ def test_nonpareil(run):
     )
 
 
+
+def test_ngsbits_samplesimilarity(run):
+    run(
+        "bio/ngsbits/samplesimilarity",
+        [
+            "snakemake", 
+            "--cores", 
+            "1", 
+            "--use-conda", 
+            "-F", 
+            "similarity.tsv",
+        ],
+    )
+
+
 def test_nonpareil_plot(run):
     run(
         "bio/nonpareil/plot",