feat: add wrapper for MEGAHIT

bio/megahit/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - megahit =1.2.9
+  - snakemake-wrapper-utils =0.7.2

bio/megahit/meta.yaml

@@ -0,0 +1,23 @@
+name: "megahit"
+
+url: https://github.com/voutcn/megahit
+
+description: |
+  MEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.
+  Input options that can be specified for multiple times (supporting plain text and gz/bz2 extensions).
+
+input:
+  - reads: list of reads in FASTQ format
+  - r1: forward reads
+  - r2: reverse reads
+  - interleaved: interleaved reads
+  - unpaired: unpaired reads
+
+output:
+  - contigs: output file with contigs
+  - log: log file
+  - json: options json file
+
+authors:
+  - Jie Zhu
+  - Filipe G. Vieira

bio/megahit/test/Snakefile

@@ -0,0 +1,29 @@
+container: "docker://continuumio/miniconda3:4.4.10"
+
+
+rule run_megahit:
+    input:
+        reads=["test_reads/sample1_R1.fastq.gz", "test_reads/sample1_R2.fastq.gz"],
+    output:
+        contigs="assembly/contigs.fasta",
+    benchmark:
+        "logs/benchmarks/assembly/megahit.txt"
+    params:
+        # all parameters are optional
+        extra="--min-count 10 --k-list 21,29,39,59,79,99,119,141",
+    log:
+        "logs/megahit.log",
+    threads: 8
+    resources:
+        mem_mb=250000,
+    wrapper:
+        "master/bio/megahit"
+
+
+rule download_test_reads:
+    output:
+        ["test_reads/sample1_R1.fastq.gz", "test_reads/sample1_R2.fastq.gz"],
+    log:
+        "logs/download.log",
+    shell:
+        "(wget -O - https://zenodo.org/record/3992790/files/test_reads.tar.gz | tar -xzf -) > {log} 2>&1"

bio/megahit/wrapper.py

@@ -0,0 +1,73 @@
+"""Snakemake wrapper for megahit."""
+
+__author__ = "Jie Zhu @alienzj"
+__copyright__ = "Copyright 2025, Jie Zhu"
+__email__ = "[email protected]"
+__license__ = "MIT"
+
+import os, tempfile, shutil
+from snakemake.shell import shell
+from snakemake_wrapper_utils.snakemake import get_mem
+
+# get output_dir and files from output
+output_dir = os.path.split(snakemake.output[0])[0]
+contigs_file = snakemake.output.get("contigs", os.path.join(output_dir, "contigs.fa"))
+contigs_file_original = os.path.join(output_dir, "final.contigs.fa")
+options_file = snakemake.output.get("options", os.path.join(output_dir, "options.json"))
+log_file = snakemake.output.get("log", os.path.join(output_dir, "log"))
+
+# parse params
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+memory_requirements = get_mem(snakemake, out_unit="KiB") * 1024
+
+# parse short reads
+if hasattr(snakemake.input, "reads"):
+    reads = snakemake.input.reads
+else:
+    reads = snakemake.input
+
+input_arg = ""
+
+# handle named inputs if available
+if hasattr(snakemake.input, "r1") and hasattr(snakemake.input, "r2"):
+    input_arg += " -1 {} -2 {} ".format(snakemake.input.r1, snakemake.input.r2)
+elif len(reads) >= 2:
+    input_arg += " -1 {} -2 {} ".format(reads[0], reads[1])
+
+# handle interleaved reads if specified
+if hasattr(snakemake.input, "interleaved"):
+    input_arg += " --12 {} ".format(snakemake.input.interleaved)
+elif len(reads) >= 3 and not hasattr(snakemake.input, "r1"):
+    input_arg += " --12 {} ".format(reads[2])
+
+# handle additional reads if specified
+if hasattr(snakemake.input, "unpaired"):
+    input_arg += " --read {} ".format(snakemake.input.unpaired)
+elif len(reads) >= 4 and not hasattr(snakemake.input, "r1"):
+    input_arg += " --read {} ".format(reads[3])
+
+
+with tempfile.TemporaryDirectory(dir=os.path.dirname(output_dir)) as temp_dir:
+    output_temp_dir = os.path.join(temp_dir, "temp")
+
+    shell(
+        "megahit "
+        " -t {snakemake.threads} "
+        " -m {memory_requirements} "
+        " -o {output_temp_dir} "
+        " {input_arg} "
+        " {extra} "
+        " > {snakemake.log[0]} 2>&1 "
+    )
+
+    if os.path.exists(os.path.join(output_temp_dir, "done")):
+        shell("rm -rf {output_dir}")
+        shutil.move(output_temp_dir, output_dir)
+
+        if (
+            os.path.exists(contigs_file_original)
+            and os.path.exists(options_file)
+            and os.path.exists(log_file)
+        ):
+            shutil.move(contigs_file_original, contigs_file)

test_wrappers.py

@@ -6398,6 +6398,20 @@ def test_metaspades(run):
     )
 
 
+def test_megahit(run):
+    run(
+        "bio/megahit",
+        [
+            "snakemake",
+            "run_megahit",
+            "--cores",
+            "2",
+            "--use-conda",
+            "-F",
+        ],
+    )
+
+
 def test_verifybamid2(run):
     run(
         "bio/verifybamid/verifybamid2",