From 056bcc7494d113cc47a323fdf40ca41b6a31e782 Mon Sep 17 00:00:00 2001
From: fgvieira <1151762+fgvieira@users.noreply.github.com>
Date: Tue, 19 Sep 2023 15:18:52 +0200
Subject: [PATCH] Add ngsngs wrapper

---
 bio/ngsngs/environment.yaml  |  6 ++++
 bio/ngsngs/meta.yaml         | 11 +++++++
 bio/ngsngs/test/Snakefile    | 60 ++++++++++++++++++++++++++++++++++++
 bio/ngsngs/test/genome.fasta |  2 ++
 bio/ngsngs/wrapper.py        | 21 +++++++++++++
 test.py                      | 32 +++++++++++++++++++
 6 files changed, 132 insertions(+)
 create mode 100644 bio/ngsngs/environment.yaml
 create mode 100644 bio/ngsngs/meta.yaml
 create mode 100644 bio/ngsngs/test/Snakefile
 create mode 100644 bio/ngsngs/test/genome.fasta
 create mode 100644 bio/ngsngs/wrapper.py

diff --git a/bio/ngsngs/environment.yaml b/bio/ngsngs/environment.yaml
new file mode 100644
index 00000000000..00511f60640
--- /dev/null
+++ b/bio/ngsngs/environment.yaml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - ngsngs =0.9.2
diff --git a/bio/ngsngs/meta.yaml b/bio/ngsngs/meta.yaml
new file mode 100644
index 00000000000..02850f8b512
--- /dev/null
+++ b/bio/ngsngs/meta.yaml
@@ -0,0 +1,11 @@
+name: NGSNGS
+description: Next-Generation Simulator for Next-Generation Sequencing data
+url: https://github.com/RAHenriksen/NGSNGS
+authors:
+  - Filipe G. Vieira
+input:
+  - 
+output:
+  - 
+params:
+  - tool: tool to use, either "ngsngs" (default), "LenConvert", "MisConvert", "MetaMisConvert", "RandRef", "RandVar", "QualConvert", "VCFtoBED", or "RemoveCodon"
diff --git a/bio/ngsngs/test/Snakefile b/bio/ngsngs/test/Snakefile
new file mode 100644
index 00000000000..8954086561e
--- /dev/null
+++ b/bio/ngsngs/test/Snakefile
@@ -0,0 +1,60 @@
+rule ngsngs_fq_se:
+    input:
+        "{genome}.fasta",
+    output:
+        fq="results/{genome}.SE.fq.gz",
+    log:
+        "logs/{genome}.SE.fq.log",
+    params:
+        extra="--sequencing SE --lengthdist Norm,50,20 --reads 2",
+    wrapper:
+        "master/bio/ngsngs"
+
+
+use rule ngsngs_fq_se as ngsngs_fq_pe with:
+    output:
+        fq1="results/{genome}_R1.fq.gz",
+	fq2="results/{genome}_R2.fq.gz",
+    log:
+        "logs/{genome}.PE.fq.log",
+    params:
+        extra="--sequencing PE --lengthdist Norm,50,20 --reads 2",
+
+
+use rule ngsngs_fq_se as ngsngs_bam_se with:
+    output:
+        bam="results/{genome}.SE.bam",
+    log:
+        "logs/{genome}.SE.bam.log",
+
+
+use rule ngsngs_bam_se as ngsngs_bam_pe with:
+    output:
+        bam="results/{genome}.PE.bam",
+    log:
+        "logs/{genome}.PE.bam.log",
+    params:
+        extra="--sequencing PE --lengthdist Norm,50,20 --reads 2",
+
+
+use rule ngsngs_fq_se as ngsngs_randvar with:
+    output:
+        fas="results/{genome}.randvar.fas",
+        pos="results/{genome}.randvar.pos",
+    log:
+        "logs/{genome}.randvar.log",
+    params:
+        tool="RandVar",
+        extra="--modulus 2",
+
+
+rule ngsngs_randref:
+    output:
+        fas="results/{genome}.randref.fas",
+    log:
+        "logs/{genome}.randref.log",
+    params:
+        tool="RandRef",
+        extra="--length 1000 --chrNo 2 --NoNt --NoStopCodon",
+    wrapper:
+        "master/bio/ngsngs"
diff --git a/bio/ngsngs/test/genome.fasta b/bio/ngsngs/test/genome.fasta
new file mode 100644
index 00000000000..308e288c979
--- /dev/null
+++ b/bio/ngsngs/test/genome.fasta
@@ -0,0 +1,2 @@
+>Sheila
+GCTAGCTCAGAAAAAAAAAA
\ No newline at end of file
diff --git a/bio/ngsngs/wrapper.py b/bio/ngsngs/wrapper.py
new file mode 100644
index 00000000000..79b3628092d
--- /dev/null
+++ b/bio/ngsngs/wrapper.py
@@ -0,0 +1,21 @@
+__author__ = "Filipe G. Vieira"
+__copyright__ = "Copyright 2023, Filipe G. Vieira"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
+
+tool = snakemake.params.get("tool", "ngsngs")
+assert tool in ["ngsngs", "LenConvert", "MisConvert", "MetaMisConvert", "RandRef", "RandVar", "QualConvert", "VCFtoBED", "RemoveCodon"], "invalid tool specified"
+
+threads = f"--threads {snakemake.threads}" if tool == "ngsngs" else ""
+
+input = f"--input {snakemake.input[0]}" if len(snakemake.input) else ""
+
+output = ",".join([str(value) for key, value in snakemake.output.items() if key != "pos"])
+output_extra = " ".join([f"--{key} {value}" for key, value in snakemake.output.items() if key == "pos"])
+
+
+shell("{tool} {threads} {input} {extra} --output {output} {output_extra} {log}")
diff --git a/test.py b/test.py
index 054b9bd8cc0..5c16d2b1ae1 100644
--- a/test.py
+++ b/test.py
@@ -139,6 +139,38 @@ def run(wrapper, cmd, check_log=None):
             os.chdir(origdir)
 
 
+@skip_if_not_modified
+def test_ngsngs():
+    run(
+        "bio/ngsngs",
+        [
+            "snakemake",
+            "--cores",
+            "2",
+            "--use-conda",
+            "-F",
+            "results/genome.SE.fq.gz",
+            "results/genome_R1.fq.gz",
+            "results/genome_R2.fq.gz",
+            "results/genome.SE.bam",
+            "results/genome.PE.bam",
+        ],
+    )
+
+    run(
+        "bio/ngsngs",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "-F",
+            "results/genome.randvar.pos",
+            "results/genome.randref.fas"
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_galah():
     run(