/
phase_multiome.smk
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/
phase_multiome.smk
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import os
RNASAMPLES, = glob_wildcards(config['fqdir_rna'] + '/{sample}_R1.fastq.gz')
ATACSAMPLES, = glob_wildcards(config['fqdir_atac'] + '/{sample}_a_I1.fastq.gz')
IX=['a', 'b', 'c', 'd']
rule all:
input:
expand(
'splitFQ_RNA/{rnasample}_g1_S1_L001_R1_001.fastq.gz',
rnasample=RNASAMPLES
),
expand(
'splitFQ_ATAC/{atacsample}_{ix}_g1_S1_L001_R1_001.fastq.gz',
atacsample=ATACSAMPLES,
ix=IX
)
rule STAR:
input:
config['fqdir_rna'] + '/{rnasample}_R2.fastq.gz'
output:
temp('STAR/{rnasample}.bam')
params:
gdir = config['star_ix'],
sname = lambda wildcards: 'STAR/' + wildcards.rnasample
threads: 25
shell:'''
STAR --genomeDir {params.gdir} \
--runThreadN {threads} \
--readFilesCommand zcat \
--outFileNamePrefix {params.sname} \
--readFilesIn {input} \
--outSAMattributes NH HI NM MD \
--outSAMtype BAM Unsorted
mv {params.sname}Aligned.out.bam {params.sname}.bam
'''
rule bt2:
input:
R1 = config['fqdir_atac'] + '/{atacsample}_{ix}_R1.fastq.gz',
R2 = config['fqdir_atac'] + '/{atacsample}_{ix}_R2.fastq.gz'
output:
temp('bowtie2/{atacsample}_{ix}.bam')
params:
btix = config['bt_ix']
threads: 25
shell:'''
bowtie2 -X 1000 -x {params.btix} -1 {input.R1} -2 {input.R2} -p {threads} | samtools view -Sb - | samtools sort -n -m 25G -@ 2 -O bam - > {output}
'''
rule splitATAC:
input:
'bowtie2/{atacsample}_{ix}.bam'
output:
g1 = temp('SNPsplit_ATAC/{atacsample}_{ix}.genome1.bam'),
g2 = temp('SNPsplit_ATAC/{atacsample}_{ix}.genome2.bam')
params:
snpfile = config['snpfile']
threads: 15
shell:'''
SNPsplit --snp_file {params.snpfile} --no_sort --paired -o SNPsplit_ATAC {input}
'''
rule splitRNA:
input:
'STAR/{rnasample}.bam'
output:
g1 = temp('SNPsplit_RNA/{rnasample}.genome1.bam'),
g2 = temp('SNPsplit_RNA/{rnasample}.genome2.bam')
params:
snpfile = config['snpfile']
threads: 15
shell:'''
SNPsplit --single_end --snp_file {params.snpfile} -o SNPsplit_RNA {input}
'''
rule ixATAC:
input:
g1 = 'SNPsplit_ATAC/{atacsample}_{ix}.genome1.bam',
g2 = 'SNPsplit_ATAC/{atacsample}_{ix}.genome2.bam'
output:
g1 = temp('SNPsplit_ATAC/{atacsample}_{ix}.g1.ix.gz'),
g2 = temp('SNPsplit_ATAC/{atacsample}_{ix}.g2.ix.gz')
threads: 2
shell:'''
samtools view {input.g1} | cut -f1 | gzip > {output.g1}
samtools view {input.g2} | cut -f1 | gzip > {output.g2}
'''
rule ixRNA:
input:
g1 = 'SNPsplit_RNA/{rnasample}.genome1.bam',
g2 = 'SNPsplit_RNA/{rnasample}.genome2.bam'
output:
g1 = temp('SNPsplit_RNA/{rnasample}.g1.ix.gz'),
g2 = temp('SNPsplit_RNA/{rnasample}.g2.ix.gz')
threads: 2
shell:'''
samtools view {input.g1} | cut -f1 | gzip > {output.g1}
samtools view {input.g2} | cut -f1 | gzip > {output.g2}
'''
rule splitfq_rna:
input:
g1 = 'SNPsplit_RNA/{rnasample}.g1.ix.gz',
g2 = 'SNPsplit_RNA/{rnasample}.g2.ix.gz'
output:
R1_g1 = 'splitFQ_RNA/{rnasample}_g1_S1_L001_R1_001.fastq.gz',
R2_g1 = 'splitFQ_RNA/{rnasample}_g1_S1_L001_R2_001.fastq.gz',
R1_g2 = 'splitFQ_RNA/{rnasample}_g2_S1_L001_R1_001.fastq.gz',
R2_g2 = 'splitFQ_RNA/{rnasample}_g2_S1_L001_R2_001.fastq.gz'
threads: 8
params:
spfq = 'python ' + config['splitfq'],
R1 = lambda wildcards: config['fqdir_rna'] + '/{}_R1.fastq.gz'.format(wildcards.rnasample),
R2 = lambda wildcards: config['fqdir_rna'] + '/{}_R2.fastq.gz'.format(wildcards.rnasample)
shell:'''
{params.spfq} --fq {params.R1} --ix {input.g1} | gzip > {output.R1_g1}&
{params.spfq} --fq {params.R2} --ix {input.g1} | gzip > {output.R2_g1}&
{params.spfq} --fq {params.R1} --ix {input.g2} | gzip > {output.R1_g2}&
{params.spfq} --fq {params.R2} --ix {input.g2} | gzip > {output.R2_g2}&
'''
rule splitfq_atac:
input:
g1 = 'SNPsplit_ATAC/{atacsample}_{ix}.g1.ix.gz',
g2 = 'SNPsplit_ATAC/{atacsample}_{ix}.g2.ix.gz'
output:
R1_g1 = 'splitFQ_ATAC/{atacsample}_{ix}_g1_S1_L001_R1_001.fastq.gz',
R2_g1 = 'splitFQ_ATAC/{atacsample}_{ix}_g1_S1_L001_R2_001.fastq.gz',
I1_g1 = 'splitFQ_ATAC/{atacsample}_{ix}_g1_S1_L001_I1_001.fastq.gz',
I2_g1 = 'splitFQ_ATAC/{atacsample}_{ix}_g1_S1_L001_I2_001.fastq.gz',
R1_g2 = 'splitFQ_ATAC/{atacsample}_{ix}_g2_S1_L001_R1_001.fastq.gz',
R2_g2 = 'splitFQ_ATAC/{atacsample}_{ix}_g2_S1_L001_R2_001.fastq.gz',
I1_g2 = 'splitFQ_ATAC/{atacsample}_{ix}_g2_S1_L001_I1_001.fastq.gz',
I2_g2 = 'splitFQ_ATAC/{atacsample}_{ix}_g2_S1_L001_I2_001.fastq.gz'
threads: 16
params:
spfq = 'python ' + config['splitfq'],
R1 = lambda wildcards: config['fqdir_atac'] + '/{}_{}_R1.fastq.gz'.format(wildcards.atacsample, wildcards.ix),
R2 = lambda wildcards: config['fqdir_atac'] + '/{}_{}_R2.fastq.gz'.format(wildcards.atacsample, wildcards.ix),
I1 = lambda wildcards: config['fqdir_atac'] + '/{}_{}_I1.fastq.gz'.format(wildcards.atacsample, wildcards.ix),
I2 = lambda wildcards: config['fqdir_atac'] + '/{}_{}_I2.fastq.gz'.format(wildcards.atacsample, wildcards.ix)
shell:'''
{params.spfq} --fq {params.R1} --ix {input.g1} | gzip > {output.R1_g1}&
{params.spfq} --fq {params.R2} --ix {input.g1} | gzip > {output.R2_g1}&
{params.spfq} --fq {params.I1} --ix {input.g1} | gzip > {output.I1_g1}&
{params.spfq} --fq {params.I2} --ix {input.g1} | gzip > {output.I2_g1}&
{params.spfq} --fq {params.R1} --ix {input.g2} | gzip > {output.R1_g2}&
{params.spfq} --fq {params.R2} --ix {input.g2} | gzip > {output.R2_g2}&
{params.spfq} --fq {params.I1} --ix {input.g2} | gzip > {output.I1_g2}&
{params.spfq} --fq {params.I2} --ix {input.g2} | gzip > {output.I2_g2}
'''