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cmazzoni
Genome_Evaluation_Pipeline
Commits
751365d6
Commit
751365d6
authored
2 years ago
by
james94
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build illumina changes
parent
8b3024b7
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rules/build_illumina.smk
+50
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rules/build_illumina.smk
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rules/build_illumina.smk
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View file @
751365d6
...
...
@@ -23,7 +23,7 @@ rule unzipFastq_R1:
input:
assembly=R1_gzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"),
conda:
...
...
@@ -42,7 +42,7 @@ rule symlinkUnzippedFastq_R1:
input:
assembly=R1_notgzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R1.fastq"),
container:
None
shell:
...
...
@@ -54,7 +54,7 @@ rule unzipFastq_R2:
input:
assembly=R2_gzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
conda:
...
...
@@ -73,7 +73,7 @@ rule symlinkUnzippedFastq_R2:
input:
assembly=R2_notgzipped,
output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.{trim10x}.{trimAdapters}_R2.fastq"),
container:
None
shell:
...
...
@@ -84,9 +84,9 @@ rule symlinkUnzippedFastq_R2:
rule trim10xbarcodes:
input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R1.fastq"),
output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
02
_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read1.fastq"),
threads:
resource['trim10xbarcodes']['threads']
resources:
...
...
@@ -104,9 +104,9 @@ rule trim10xbarcodes:
rule symlink_trim10xbarcodesR2:
input:
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
01
_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.10xTrimmed.{trimAdapters}_R2.fastq")
output:
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
02
_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.10xTrimmed.{trimAdapters}_Read2.fastq")
container:
None
shell:
...
...
@@ -118,11 +118,11 @@ rule symlink_trim10xbarcodesR2:
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"),
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.fastq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_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")
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq")
container:
None
shell:
...
...
@@ -133,11 +133,11 @@ rule symLink_trim10xbarcodes_notrimAdapt:
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")
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_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")
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq")
container:
None
shell:
...
...
@@ -148,11 +148,11 @@ rule symlinks_no10xOrAdaptTrim:
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")
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.fastq"),
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
temp
_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")
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.fastq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq")
container:
None
shell:
...
...
@@ -163,14 +163,14 @@ rule symlinks_no10xwithAdaptTrim:
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"),
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.fastq"),
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
params:
outputDir=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
02
_trimReads/"),
outputDir=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_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"))
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.fq")),
read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
threads:
resource['trimAdapters']['threads']
resources:
...
...
@@ -187,13 +187,13 @@ rule trimAdapters:
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")
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"),
read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
params:
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
04_
fastqc")
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
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")
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"),
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
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:
...
...
@@ -208,16 +208,16 @@ rule fastqc_Illumina:
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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2])
read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_1_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
fastqc/{readCounter}.{trim10x}.{trimAdapters}_val_2_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[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"
folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
fastqc/"),
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
multiqc/"),
filename="{sample}.multiqcReport.html"
output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
05_
multiqc/{sample}.
{trim10x}.{trimAdapters}.
multiqcReport.html")
os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
QC/
multiqc/{sample}.multiqcReport.html")
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.
{trim10x}.{trimAdapters}_
multiqc.log")
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.multiqc.log")
conda:
os.path.join(workflow.basedir, "envs/pigz.yaml")
shell:
...
...
@@ -227,7 +227,7 @@ rule multiqc_hifi:
rule meryl_R1:
input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
02
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq")
params:
kmer = "{kmer}",
threads:
...
...
@@ -236,7 +236,7 @@ rule meryl_R1:
mem_mb=resource['meryl_R1']['mem_mb'],
time=resource['meryl_R1']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
03_
merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"))
temp(
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/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:
...
...
@@ -251,7 +251,7 @@ rule meryl_R1:
rule meryl_R2:
input:
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
02
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq")
params:
kmer = "{kmer}",
threads:
...
...
@@ -260,7 +260,7 @@ rule meryl_R2:
mem_mb=resource['meryl_R2']['mem_mb'],
time=resource['meryl_R2']['time'],
output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
03_
merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"))
temp(
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/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:
...
...
@@ -276,24 +276,24 @@ rule meryl_R2:
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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[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=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2])
#
removeReads1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_1.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
#
removeReads2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/{readCounter}.{trim10x}.{trimAdapters}_val_2.fq"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], trimAdapters=dictSamples[wildcards.sample][2]),
read1=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R1.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[wildcards.sample][2]),
read2=lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/merylDb/{readCounter}.{trim10x}.{trimAdapters}_R2.{kmer}.meryl"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], trim10x=dictSamples[wildcards.sample][1], kmer=dictSamples[wildcards.sample][0], trimAdapters=dictSamples[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/"),
removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_trimReads/"),
removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/
temp
_unzipFastqs/"),
kmer = "{kmer}",
path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/
03_
merylDb/")
path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/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")),
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/complete_
illumina.{sample
}.{kmer}.meryl")),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}
_hifi_{kmer}.{trim10x}.{trimAdapt
er
s
}.log")
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}
.illumina_meryl.{km
er}.log")
priority:
10
conda:
...
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