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sbx_assembly.smk
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sbx_assembly.smk
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# -*- mode: Snakemake -*-
#
# Contig building and other assembly rules
#
# Requires Megahit.
TARGET_ASSEMBLY = [
expand(ASSEMBLY_FP / "contigs" / "{sample}-contigs.fa", sample=Samples.keys()),
expand(
ANNOTATION_FP / "genes" / "prodigal" / "{sample}_genes_{suffix}.fa",
sample=Samples.keys(),
suffix=["prot", "nucl"],
),
]
def get_assembly_ext_path() -> Path:
ext_path = Path(sunbeam_dir) / "extensions" / "sbx_assembly"
if ext_path.exists():
return ext_path
raise Error(
"Filepath for assembly not found, are you sure it's installed under extensions/sbx_assembly?"
)
SBX_ASSEMBLY_VERSION = open(get_assembly_ext_path() / "VERSION").read().strip()
try:
BENCHMARK_FP
except NameError:
BENCHMARK_FP = output_subdir(Cfg, "benchmarks")
try:
LOG_FP
except NameError:
LOG_FP = output_subdir(Cfg, "logs")
rule all_assembly:
"""Build contigs for all samples."""
input:
TARGET_ASSEMBLY,
ruleorder: megahit_paired > megahit_unpaired
rule megahit_paired:
input:
r1=QC_FP / "decontam" / "{sample}_1.fastq.gz",
r2=QC_FP / "decontam" / "{sample}_2.fastq.gz",
output:
ASSEMBLY_FP / "megahit" / "{sample}_asm" / "final.contigs.fa",
benchmark:
BENCHMARK_FP / "megahit_paired_{sample}.tsv"
log:
LOG_FP / "megahit_paired_{sample}.log",
params:
out_fp=str(ASSEMBLY_FP / "megahit" / "{sample}_asm"),
threads: 4
conda:
"envs/sbx_assembly.yml"
container:
f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
shell:
"""
## turn off bash strict mode
set +o pipefail
## sometimes the error is due to lack of memory
exitcode=0
if [ -d {params.out_fp} ]
then
echo "Clearing previous megahit directory..." > {log}
rm -rf {params.out_fp}
fi
megahit -t {threads} -1 {input.r1} -2 {input.r2} -o {params.out_fp} --continue 2>&1 {log} || exitcode=$?
if [ $exitcode -eq 255 ]
then
touch {output}
echo "Empty contigs" 2>&1 | tee {log}
elif [ $exitcode -gt 1 ]
then
echo "Check your memory" 2>&1 | tee {log}
fi
"""
rule megahit_unpaired:
input:
QC_FP / "decontam" / "{sample}_1.fastq.gz",
output:
ASSEMBLY_FP / "megahit" / "{sample}_asm" / "final.contigs.fa",
benchmark:
BENCHMARK_FP / "megahit_unpaired_{sample}.tsv"
log:
LOG_FP / "megahit_unpaired_{sample}.log",
params:
out_fp=str(ASSEMBLY_FP / "megahit" / "{sample}_asm"),
threads: 4
conda:
"envs/sbx_assembly.yml"
container:
f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
shell:
"""
## turn off bash strict mode
set +o pipefail
## sometimes the error is due to lack of memory
exitcode=0
megahit -t {threads} -r {input} -o {params.out_fp} -f --continue 2>&1 {log} || exitcode=$?
if [ $exitcode -eq 255 ]
then
echo "Empty contigs"
touch {output}
elif [ $exitcode -gt 1 ]
then
echo "Check your memory"
fi
"""
rule final_filter:
input:
ASSEMBLY_FP / "megahit" / "{sample}_asm" / "final.contigs.fa",
output:
ASSEMBLY_FP / "contigs" / "{sample}-contigs.fa",
log:
LOG_FP / "final_filter_{sample}.log",
benchmark:
BENCHMARK_FP / "final_filter_{sample}.tsv"
params:
len=Cfg["sbx_assembly"]["min_length"],
script:
"scripts/final_filter.py"
rule clean_assembly:
input:
M=ASSEMBLY_FP / "megahit",
shell:
"""
rm -rf {input.M} && echo "Cleanup assembly finished."
"""
rule prodigal:
"""Use Progial for coding genes predictions in contigs."""
input:
ASSEMBLY_FP / "contigs" / "{sample}-contigs.fa",
output:
gff=ANNOTATION_FP / "genes" / "prodigal" / "{sample}_genes.gff",
faa=ANNOTATION_FP / "genes" / "prodigal" / "{sample}_genes_prot.fa",
fna=ANNOTATION_FP / "genes" / "prodigal" / "{sample}_genes_nucl.fa",
benchmark:
BENCHMARK_FP / "prodigal_{sample}.tsv"
log:
LOG_FP / "prodigal_{sample}.log",
conda:
"envs/sbx_assembly.yml"
container:
f"docker://sunbeamlabs/sbx_assembly:{SBX_ASSEMBLY_VERSION}-assembly"
shell:
"""
if [[ -s {input} ]]; then
prodigal -i {input} -o {output.gff} \
-a {output.faa} -d {output.fna} -p meta 2>&1 | tee {log}
else
touch {output.faa}
touch {output.gff}
touch {output.fna}
fi
"""
rule _test_prodigal:
input:
expand(
ANNOTATION_FP / "genes" / "prodigal" / "{sample}_genes_{suffix}.fa",
sample=Samples.keys(),
suffix=["prot", "nucl"],
),