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add minimap2 aligner #143

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Mar 31, 2023
Merged

add minimap2 aligner #143

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7 changes: 7 additions & 0 deletions workflow/envs/minimap_align.yaml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- minimap2=2.24
- samtools=1.10
102 changes: 102 additions & 0 deletions workflow/rules/align.smk
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Expand Up @@ -629,6 +629,108 @@ elif config.general["aligner"] == "bowtie":
{params.SAMTOOLS} view -h -F 4 -F 2048 -o "{output.REF}" "{output.TMP_SAM} 2> >(tee -a {log.errfile} >&2)
"""

elif config.general["aligner"] == "minimap":

rule ref_minimap_index:
input:
reference_file,
output:
reference_file+'.mmi',
params:
MINIMAP=config.applications["minimap"],
log:
outfile="references/minimap.index.out.log",
errfile="references/minimap.index.err.log",
conda:
config.ref_minimap_index["conda"]
benchmark:
"references/ref_minimap_index.benchmark"
group:
"align"
resources:
disk_mb=1250,
mem_mb=config.ref_minimap_index["mem"],
runtime=config.ref_minimap_index["time"],
threads: 1
shell:
"""
{params.MINIMAP} -t {threads} -d {output} {input} 2> >(tee {log.errfile} >&2)
"""

if config.input["paired"]:

rule minimap_align:
input:
target=reference_file+'.mmi',
# FASTQ=input_align_gz,
R1="{dataset}/preprocessed_data/R1.fastq.gz",
R2="{dataset}/preprocessed_data/R2.fastq.gz",

# INDEX=multiext(reference_file,*bwa_idx_ext),
output:
REF=temp_with_prefix("{dataset}/alignments/REF_aln.sam"),
TMP_SAM=temp_with_prefix("{dataset}/alignments/tmp_aln.sam"),
params:
EXTRA=config.minimap_align["extra"],
PRESET=config.minimap_align["preset"],
MINIMAP=config.applications["minimap"],
SAMTOOLS=config.applications["samtools"],
log:
outfile="{dataset}/alignments/minimap_align.log",
errfile="{dataset}/alignments/minimap_align.err.log",
conda:
config.minimap_align["conda"]
benchmark:
"{dataset}/alignments/minimap_align.benchmark"
group:
"align"
resources:
disk_mb=1250,
mem_mb=config.minimap_align["mem"],
runtime=config.minimap_align["time"],
threads: config.minimap_align["threads"]
shell:
"""
{params.MINIMAP} -t {threads} -a -x {params.PRESET} {input.target} {input.R1} {input.R2} > {output.TMP_SAM} 2> >(tee -a {log.errfile} >&2)
{params.SAMTOOLS} view -h -f 2 -F 2048 -o "{output.REF}" "{output.TMP_SAM}" 2> >(tee -a {log.errfile} >&2)
"""
else:

rule minimap_align_se:
input:
target=reference_file+'.mmi',
# FASTQ=input_align_gz,
R1="{dataset}/preprocessed_data/R1.fastq.gz",
# R2="{dataset}/preprocessed_data/R2.fastq.gz",

# INDEX=multiext(reference_file,*bwa_idx_ext),
output:
REF=temp_with_prefix("{dataset}/alignments/REF_aln.sam"),
TMP_SAM=temp_with_prefix("{dataset}/alignments/tmp_aln.sam"),
params:
EXTRA=config.minimap_align["extra"],
PRESET=config.minimap_align["preset"],
MINIMAP=config.applications["minimap"],
SAMTOOLS=config.applications["samtools"],
log:
outfile="{dataset}/alignments/minimap_align.log",
errfile="{dataset}/alignments/minimap_align.err.log",
conda:
config.minimap_align["conda"]
benchmark:
"{dataset}/alignments/minimap_align.benchmark"
group:
"align"
resources:
disk_mb=1250,
mem_mb=config.minimap_align["mem"],
runtime=config.minimap_align["time"],
threads: config.minimap_align["threads"]
shell:
"""
{params.MINIMAP} -t {threads} -a -x {params.PRESET} {params.EXTRA} {input.target} {input.R1} > {output.TMP_SAM} 2> >(tee -a {log.errfile} >&2)
{params.SAMTOOLS} view -h -f 2 -F 2048 -o "{output.REF}" "{output.TMP_SAM}" 2> >(tee -a {log.errfile} >&2)
"""

# NOTE ngshmmalignb also generate consensus so check there too.
# if config.general["aligner"] == "ngshmmalign":
Expand Down
55 changes: 54 additions & 1 deletion workflow/schemas/config_schema.json
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Expand Up @@ -16,7 +16,7 @@
},
"aligner": {
"type": "string",
"enum": ["ngshmmalign","bwa","bowtie"],
"enum": ["ngshmmalign","bwa","bowtie","minimap"],
"default": "ngshmmalign",
"description": "There are three options for mapping reads, either using [`ngshmmalign`](https://github.com/cbg-ethz/ngshmmalign), [BWA MEM (`bwa`)](https://github.com/lh3/bwa) [^1], or [Bowtie 2 (`bowtie`)](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) [^2]. To use a different aligner than the default, indicate which aligner you want to use by setting the property aligner.\n\n[^1]: Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013.\n[^2]: Langmead, B. and Salzberg, S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012.\n\n**Note**: Some virus-specific base configuration specified in `virus_base_config` might change this option's default to a more appropriate aligner for that virus, e.g., depending on its usual diversity and mutation rate.\nYou are still free to override that default in your configuration shall the need arise.",
"examples": ["bowtie"]
Expand Down Expand Up @@ -311,6 +311,10 @@
"type": "string",
"default": "bowtie2"
},
"minimap": {
"type": "string",
"default": "minimap2"
},
"samtools": {
"type": "string",
"default": "samtools"
Expand Down Expand Up @@ -786,6 +790,55 @@
"default": {},
"type": "object"
},
"ref_minimap_index": {
"properties": {
"mem": {
"type": "integer",
"default": 2000
},
"time": {
"type": "integer",
"default": 235
},
"conda": {
"type": "string",
"default": "{VPIPE_BASEDIR}/envs/minimap_align.yaml"
}
},
"default": {},
"type": "object"
},
"minimap_align": {
"properties": {
"mem": {
"type": "integer",
"default": 1250
},
"time": {
"type": "integer",
"default": 235
},
"threads": {
"type": "integer"
},
"preset": {
"type": "string",
"default": "sr",
"description": "Specify minimap2 presets."
},
"conda": {
"type": "string",
"default": "{VPIPE_BASEDIR}/envs/minimap_align.yaml"
},
"extra": {
"type": "string",
"default": "",
"description": "With property `extra`, users can pass additional options to run minimap2. For more details on minimap2 configurable options refer to the software [documentation](https://github.com/lh3/minimap2)."
}
},
"default": {},
"type": "object"
},
"primerstrim" : {
"properties": {
"mem": {
Expand Down