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

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rules/build_illumina.smk
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......@@ -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}.{trimAdapters}.log")
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.illumina_meryl.{kmer}.log")
priority:
10
conda:
......
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