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Commit 751365d6 authored by james94's avatar james94
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build illumina changes

parent 8b3024b7
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...@@ -23,7 +23,7 @@ rule unzipFastq_R1: ...@@ -23,7 +23,7 @@ rule unzipFastq_R1:
input: input:
assembly=R1_gzipped, assembly=R1_gzipped,
output: 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: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"), os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R1_pigzUnzip.log"),
conda: conda:
...@@ -42,7 +42,7 @@ rule symlinkUnzippedFastq_R1: ...@@ -42,7 +42,7 @@ rule symlinkUnzippedFastq_R1:
input: input:
assembly=R1_notgzipped, assembly=R1_notgzipped,
output: 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: container:
None None
shell: shell:
...@@ -54,7 +54,7 @@ rule unzipFastq_R2: ...@@ -54,7 +54,7 @@ rule unzipFastq_R2:
input: input:
assembly=R2_gzipped, assembly=R2_gzipped,
output: 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: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_R2_pigzUnzip.log")
conda: conda:
...@@ -73,7 +73,7 @@ rule symlinkUnzippedFastq_R2: ...@@ -73,7 +73,7 @@ rule symlinkUnzippedFastq_R2:
input: input:
assembly=R2_notgzipped, assembly=R2_notgzipped,
output: 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: container:
None None
shell: shell:
...@@ -84,9 +84,9 @@ rule symlinkUnzippedFastq_R2: ...@@ -84,9 +84,9 @@ rule symlinkUnzippedFastq_R2:
rule trim10xbarcodes: rule trim10xbarcodes:
input: 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: 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: threads:
resource['trim10xbarcodes']['threads'] resource['trim10xbarcodes']['threads']
resources: resources:
...@@ -104,9 +104,9 @@ rule trim10xbarcodes: ...@@ -104,9 +104,9 @@ rule trim10xbarcodes:
rule symlink_trim10xbarcodesR2: rule symlink_trim10xbarcodesR2:
input: 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: 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: container:
None None
shell: shell:
...@@ -118,11 +118,11 @@ rule symlink_trim10xbarcodesR2: ...@@ -118,11 +118,11 @@ rule symlink_trim10xbarcodesR2:
rule symLink_trim10xbarcodes_notrimAdapt: rule symLink_trim10xbarcodes_notrimAdapt:
input: input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read1.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/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"), read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
output: output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_1.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/02_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq") read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_val_2.fq")
container: container:
None None
shell: shell:
...@@ -133,11 +133,11 @@ rule symLink_trim10xbarcodes_notrimAdapt: ...@@ -133,11 +133,11 @@ rule symLink_trim10xbarcodes_notrimAdapt:
rule symlinks_no10xOrAdaptTrim: rule symlinks_no10xOrAdaptTrim:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R1.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/01_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq") read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
output: output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_1.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/02_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq") read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.notAdaptTrimmed_val_2.fq")
container: container:
None None
shell: shell:
...@@ -148,11 +148,11 @@ rule symlinks_no10xOrAdaptTrim: ...@@ -148,11 +148,11 @@ rule symlinks_no10xOrAdaptTrim:
rule symlinks_no10xwithAdaptTrim: rule symlinks_no10xwithAdaptTrim:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R1.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/01_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq") read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
output: output:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read1.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/02_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq") read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.not10xTrimmed.AdaptTrimmed_Read2.fastq")
container: container:
None None
shell: shell:
...@@ -163,14 +163,14 @@ rule symlinks_no10xwithAdaptTrim: ...@@ -163,14 +163,14 @@ rule symlinks_no10xwithAdaptTrim:
rule trimAdapters: rule trimAdapters:
input: input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read1.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/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"), read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
params: 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", r1_prefix="{readCounter}.{trim10x}.AdaptTrimmed",
output: output:
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_1.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/02_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq")) read2=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_val_2.fq"))
threads: threads:
resource['trimAdapters']['threads'] resource['trimAdapters']['threads']
resources: resources:
...@@ -187,13 +187,13 @@ rule trimAdapters: ...@@ -187,13 +187,13 @@ rule trimAdapters:
rule fastqc_Illumina: rule fastqc_Illumina:
input: 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"),
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: 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: 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/QC/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_2_fastqc.html")
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_fastqc.log")
threads: threads:
...@@ -208,16 +208,16 @@ rule fastqc_Illumina: ...@@ -208,16 +208,16 @@ rule fastqc_Illumina:
rule multiqc_hifi: rule multiqc_hifi:
input: 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]), 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/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]) 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: params:
folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/04_fastqc/"), folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/fastqc/"),
folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/"), folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/QC/multiqc/"),
filename="{sample}.{trim10x}.{trimAdapters}.multiqcReport.html" filename="{sample}.multiqcReport.html"
output: 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: 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: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/pigz.yaml")
shell: shell:
...@@ -227,7 +227,7 @@ rule multiqc_hifi: ...@@ -227,7 +227,7 @@ rule multiqc_hifi:
rule meryl_R1: rule meryl_R1:
input: 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: params:
kmer = "{kmer}", kmer = "{kmer}",
threads: threads:
...@@ -236,7 +236,7 @@ rule meryl_R1: ...@@ -236,7 +236,7 @@ rule meryl_R1:
mem_mb=resource['meryl_R1']['mem_mb'], mem_mb=resource['meryl_R1']['mem_mb'],
time=resource['meryl_R1']['time'], time=resource['meryl_R1']['time'],
output: 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: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R1.{kmer}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R1.{kmer}.log")
priority: priority:
...@@ -251,7 +251,7 @@ rule meryl_R1: ...@@ -251,7 +251,7 @@ rule meryl_R1:
rule meryl_R2: rule meryl_R2:
input: 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: params:
kmer = "{kmer}", kmer = "{kmer}",
threads: threads:
...@@ -260,7 +260,7 @@ rule meryl_R2: ...@@ -260,7 +260,7 @@ rule meryl_R2:
mem_mb=resource['meryl_R2']['mem_mb'], mem_mb=resource['meryl_R2']['mem_mb'],
time=resource['meryl_R2']['time'], time=resource['meryl_R2']['time'],
output: 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: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R2.{kmer}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.{trimAdapters}_meryl_R2.{kmer}.log")
priority: priority:
...@@ -276,24 +276,24 @@ rule meryl_R2: ...@@ -276,24 +276,24 @@ rule meryl_R2:
rule meryl_illumina_build: rule meryl_illumina_build:
input: 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]), # 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/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]), # 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/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]), 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/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]) 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: params:
removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/02_trimReads/"), removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/"),
removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/01_unzipFastqs/"), removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/"),
kmer = "{kmer}", 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: threads:
resource['meryl_illumina_build']['threads'] resource['meryl_illumina_build']['threads']
resources: resources:
mem_mb=resource['meryl_illumina_build']['mem_mb'], mem_mb=resource['meryl_illumina_build']['mem_mb'],
time=resource['meryl_illumina_build']['time'], time=resource['meryl_illumina_build']['time'],
output: 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: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}_hifi_{kmer}.{trim10x}.{trimAdapters}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.illumina_meryl.{kmer}.log")
priority: priority:
10 10
conda: conda:
......
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