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Commit 775aa95a authored by james94's avatar james94
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Deleted testUpload.txt, testUpload2.text, rules/hifi_05_11_21.smk,... 

Deleted testUpload.txt, testUpload2.text, rules/hifi_05_11_21.smk, rules/run_05_11_21.smk, rules/illumina_05_11_21.smk
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rules/hifi_05_11_21.smk deleted 100644 → 0
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localrules: symlinkUnzippedHifi, symlinkfornotSmartTrimmed, multiqc_hifi
def fq_to_trimSMRTbell(wildcards):
return trimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
def fq_to_notTrimSMRTbell(wildcards):
return notrimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
def hifi_gzipped(wildcards):
return yesGzip_hifi.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
def hifi_notgzipped(wildcards):
return noGzip_hifi.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
rule unzipHifi:
input:
fastq=hifi_gzipped,
output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
conda:
"../envs/pigz.yaml"
threads:
resource['unzipHifi']['threads']
resources:
mem_mb=resource['unzipHifi']['mem_mb'],
time=resource['unzipHifi']['time'],
shell:
"""
pigz -p {threads} -c -d -k {input.fastq} > {output} 2> {log}
"""
rule symlinkUnzippedHifi:
input:
fastq=hifi_notgzipped,
output:
temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
# threads:
# 1
shell:
"""
ln -s {input.fastq} {output}
echo "{input.fastq} no gzipped. Symlink created in place of expected decompressed file." > {log}
"""
rule trimSMRTbell:
input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.smrtTrimmed.fastq"),
output:
outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.smrtTrimmed.fastq"))
threads:
resource['trimSMRTbell']['threads']
resources:
mem_mb=resource['trimSMRTbell']['mem_mb'],
time=resource['trimSMRTbell']['time'],
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}_trimSMRTbell.log")
priority:
15
conda:
"../envs/pigz.yaml"
shell:
"""
(cutadapt -j {threads} -o {output.outputFile} {input} -b ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT -b ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --discard-trimmed) &> {log}
"""
rule symlinkfornotSmartTrimmed:
input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
output:
outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq"))
# threads:
# 1
shell:
"""
ln -s {input} {output.outputFile}
"""
rule fastqc_hifi:
input:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.{smrtornot}.fastq")
params:
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/")
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
threads:
resource['trimSMRTbell']['threads']
resources:
mem_mb=resource['fastqc_hifi']['mem_mb'],
time=resource['fastqc_hifi']['time'],
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log")
conda:
"../envs/pigz.yaml"
shell:
"""
mkdir {params.folder2out}
(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
"""
rule multiqc_hifi:
input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], smrtornot=testDict[wildcards.sample][1])
params:
folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/"),
filename="{sample}.{smrtornot}.multiqcReport.html"
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
# threads:
# 1
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.{smrtornot}.multiqc.log")
conda:
"../envs/pigz.yaml"
shell:
"(multiqc {params.folder2qc} -o {params.folder2qc} -n {params.filename}) &> {log}"
rule meryl_hifi_count:
input:
reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.{smrtornot}.fastq")
params:
kmer = "{kmer}"
threads:
resource['meryl_hifi_count']['threads']
resources:
mem_mb=resource['meryl_hifi_count']['mem_mb'],
time=resource['meryl_hifi_count']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
priority:
10
conda:
"../envs/merylMerq_2.yaml"
shell:
"""
(meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log}
"""
rule meryl_hifi_build:
input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=d[wildcards.sample], kmer=testDict[wildcards.sample][0], smrtornot=testDict[wildcards.sample][1])
params:
kmer = "{kmer}"
threads:
resource['meryl_hifi_build']['threads']
resources:
mem_mb=resource['meryl_hifi_build']['mem_mb'],
time=resource['meryl_hifi_build']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl")),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}_hifi_{smrtornot}.{kmer}.log")
priority:
10
conda:
"../envs/merylMerq_2.yaml"
shell:
"""
(meryl union-sum {input} output {output}) &> {log}
"""
#
#
rules/illumina_05_11_21.smk deleted 100644 → 0
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− 295
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localrules: symlinkUnzippedFastq_R1, symlinkUnzippedFastq_R2, symLink_trim10xbarcodes_notrimAdapt, symlinks_no10xwithAdaptTrim, symlinks_no10xOrAdaptTrim, symlink_trim10xbarcodesR2, multiqc_hifi
def R1_gzipped(wildcards):
return yesGzip_R1.loc[(wildcards.sample, wildcards.readCounter), "Library_R1"]
def R1_notgzipped(wildcards):
return noGzip_R1.loc[(wildcards.sample, wildcards.readCounter), "Library_R1"]
def R2_gzipped(wildcards):
return yesGzip_R2.loc[(wildcards.sample, wildcards.readCounter), "Library_R2"]
def R2_notgzipped(wildcards):
return noGzip_R2.loc[(wildcards.sample, wildcards.readCounter), "Library_R2"]
rule unzipFastq_R1:
input:
assembly=R1_gzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"),
conda:
"../envs/pigz.yaml"
threads:
resource['unzipFastq_R1']['threads']
resources:
mem_mb=resource['unzipFastq_R1']['mem_mb'],
time=resource['unzipFastq_R1']['time']
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
"""
rule symlinkUnzippedFastq_R1:
input:
assembly=R1_notgzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
shell:
"""
ln -s {input} {output}
"""
rule unzipFastq_R2:
input:
assembly=R2_gzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
conda:
"../envs/pigz.yaml"
threads:
resource['unzipFastq_R2']['threads']
resources:
mem_mb=resource['unzipFastq_R2']['mem_mb'],
time=resource['unzipFastq_R2']['time']
shell:
"""
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
"""
rule symlinkUnzippedFastq_R2:
input:
assembly=R2_notgzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
shell:
"""
ln -s {input} {output}
"""
rule trim10xbarcodes:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
threads:
resource['trim10xbarcodes']['threads']
resources:
mem_mb=resource['trim10xbarcodes']['mem_mb'],
time=resource['trim10xbarcodes']['time']
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.10xTrimmed.10BarcodeRemoval_Trimmomatic.{trimAdapters}.log")
conda:
"../envs/pigz.yaml"
shell:
"""
(trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log}
"""
rule symlink_trim10xbarcodesR2:
input:
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
output:
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")
conda:
"../envs/pigz.yaml"
shell:
"""
ln -s {input.read2} {output.read2}
"""
rule symLink_trim10xbarcodes_notrimAdapt:
input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.fastq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq")
shell:
"""
ln -s {input.read1} {output.read1}
ln -s {input.read2} {output.read2}
"""
rule symlinks_no10xOrAdaptTrim:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq")
shell:
"""
ln -s {input.read1} {output.read1}
ln -s {input.read2} {output.read2}
"""
rule symlinks_no10xwithAdaptTrim:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.fastq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq")
shell:
"""
ln -s {input.read1} {output.read1}
ln -s {input.read2} {output.read2}
"""
rule trimAdapters:
input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.fastq"),
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
params:
outputDir=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/"),
r1_prefix="{readCounter}.{trim10x}.AdaptTrimmed",
output:
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.fq")),
read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
threads:
resource['trimAdapters']['threads']
resources:
mem_mb=resource['trimAdapters']['mem_mb'],
time=resource['trimAdapters']['time'],
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.AdaptTrimmed_tGalore.log")
conda:
"../envs/pigz.yaml"
shell:
"""
(trim_galore -j {threads} --basename {params.r1_prefix} --dont_gzip --length 65 -o {params.outputDir} --paired {input.read1} {input.read2}) &> {log}
"""
rule fastqc_Illumina:
input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
params:
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc")
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"),
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html")
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log")
threads:
resource['fastqc_Illumina']['threads']
resources:
mem_mb=resource['fastqc_Illumina']['mem_mb'],
time=resource['fastqc_Illumina']['time'],
conda:
"../envs/pigz.yaml"
shell:
"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}"
rule multiqc_hifi:
input:
read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2]),
read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2])
params:
folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/"),
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/"),
filename="{sample}.{trim10x}.{trimAdapters}.multiqcReport.html"
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/{sample}.{trim10x}.{trimAdapters}.multiqcReport.html")
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.{trim10x}.{trimAdapters}_multiqc.log")
conda:
"../envs/pigz.yaml"
shell:
"(multiqc {params.folder2qc} -o {params.folder2out} -n {params.filename}) &> {log}"
rule meryl_R1:
input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
params:
kmer = "{kmer}",
threads:
resource['meryl_R1']['threads']
resources:
mem_mb=resource['meryl_R1']['mem_mb'],
time=resource['meryl_R1']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl")))
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R1.{kmer}.log")
priority:
10
conda:
"../envs/merylMerq_2.yaml"
shell:
"""
export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
"""
rule meryl_R2:
input:
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
params:
kmer = "{kmer}",
threads:
resource['meryl_R2']['threads']
resources:
mem_mb=resource['meryl_R2']['mem_mb'],
time=resource['meryl_R2']['time'],
output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl")))
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R2.{kmer}.log")
priority:
10
conda:
"../envs/merylMerq_2.yaml"
shell:
"""
export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read2} output {output}) &> {log}
"""
rule meryl_illumina_build:
input:
removeReads1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2]),
removeReads2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2]),
read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], kmer=testDict[wildcards.sample][0], trimAdapters=testDict[wildcards.sample][2]),
read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/03_merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"), sample=wildcards.sample, readCounter=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], kmer=testDict[wildcards.sample][0], trimAdapters=testDict[wildcards.sample][2])
params:
removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/"),
removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/"),
kmer = "{kmer}",
path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/")
threads:
resource['meryl_illumina_build']['threads']
resources:
mem_mb=resource['meryl_illumina_build']['mem_mb'],
time=resource['meryl_illumina_build']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/complete_{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl")),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}_hifi_{kmer}.{trim10x}.{trimAdapters}.log")
priority:
10
conda:
"../envs/merylMerq_2.yaml"
shell:
"""
export OMP_NUM_THREADS={threads}
(meryl union-sum {input.read1} {input.read2} output {output}) &> {log}
rm -r {params.removeReadDIR_trimmed}
rm -r {params.removeReadDIR_unzipped}
"""
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