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Update SR DNA trimming and alignment #6

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Update SR DNA trimming and alignment #6

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6c2cf10
add minibwa and chelea
ASLeonard Jul 2, 2026
7cc2aed
fix to using index prefix
ASLeonard Jul 2, 2026
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54 changes: 52 additions & 2 deletions snakepit/short_read_alignment.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,31 @@ rule all:
expand('alignments/{sample}.{aligner}.{ext}',sample=short_read_data,ext='bam',aligner=config.get('aligners','bwa')),
expand('alignments/{sample}.{aligner}.d10.coverage',sample=short_read_data,ext='bam',aligner=config.get('aligners','bwa'))

wildcard_constraints:
aligner='bwa|strobe|minibwa|STAR'

rule chelea_filter:
input:
fastq=lambda wildcards: short_read_data[wildcards.sample]
output:
fastq=expand('trimmed/{sample}.R{N}.chelea.fastq.gz',N=(1,2),allow_missing=True)
params:
RNA_trim='--trim-polyx'
threads: 4
resources:
mem_mb_per_cpu = 2500,
runtime='4h'
shell:
'''
chelae trim --inputs {input.fastq} --outputs {output.fastq} --threads {threads} \
--filter-length 50
'''

rule fastp_filter:
input:
fastq = lambda wildcards: short_read_data[wildcards.sample]
output:
fastq = expand('fastp/{sample}.R{N}.fastq.gz',N=(1,2),allow_missing=True)
fastq = expand('trimmed/{sample}.R{N}.fastp.fastq.gz',N=(1,2),allow_missing=True)
params:
min_quality = 15,
unqualified = 40,
Expand Down Expand Up @@ -49,10 +69,40 @@ rule bwamem2_index:
index = multiext(str(Path(config['reference']).with_suffix('')),'.0123','.amb','.ann','.bwt.2bit.64','.pac')
threads: 1
resources:
mem_mb = 85000
mem_mb_per_cpu = 85000
shell:
'bwa-mem2 index {input.reference}'

rule minibwa_index:
input:
fasta = config['reference']
output:
index = multiext("index",'.l2b','.mbw')
threads: 4
resources:
mem_mb_per_cpu = 20000
shell:
'''
minibwa index -t {threads} {input.fasta} index
'''

rule minibwa_align:
input:
index=rules.minibwa_index.output['index'],
fastq=rules.chelea_filter.output['fastq']
output:
sam = pipe('alignments/{sample}.minibwa.sam')
params:
index=lambda wildcards, input: Path(input['index'][0]).with_suffix('')
threads: 12
resources:
mem_mb_per_cpu = 4000,
runtime = '4h'
shell:
'''
minibwa map -t {threads} -x sr {params.index} {input.fastq} > {output.sam}
'''

#Strobealign is quick to index on the fly and removes read-length dependency
rule strobealign_align:
input:
Expand Down