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Commit a98a21e5 authored by james94's avatar james94
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renamed envs

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rules/build_hifi.smk
+ 41
− 39
View file @ a98a21e5
localrules: symlinkUnzippedHifi, symlinkfornotSmartTrimmed, multiqc_hifi localrules: symlink_UnzippedFastq_hifi, \
symlink_noSMRTBellAdaptTrim_hifi, \
multiQC_hifi
...@@ -20,62 +22,62 @@ def hifi_notgzipped(wildcards): ...@@ -20,62 +22,62 @@ def hifi_notgzipped(wildcards):
rule unzipHifi: rule unzipFastq_hifi:
input: input:
fastq=hifi_gzipped, fastq=hifi_gzipped,
output: output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/pigzUnzip.{readCounter}.{smrtornot}.log")
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads: threads:
resource['unzipHifi']['threads'] resource['unzipFastq_hifi']['threads']
resources: resources:
mem_mb=resource['unzipHifi']['mem_mb'], mem_mb=resource['unzipFastq_hifi']['mem_mb'],
time=resource['unzipHifi']['time'], time=resource['unzipFastq_hifi']['time'],
shell: shell:
""" """
pigz -p {threads} -c -d -k {input.fastq} > {output} 2> {log} pigz -p {threads} -c -d -k {input.fastq} > {output} 2> {log}
""" """
rule symlinkUnzippedHifi: rule symlink_UnzippedFastq_hifi:
input: input:
fastq=hifi_notgzipped, fastq=hifi_notgzipped,
output: output:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/pigzUnzip.{readCounter}.{smrtornot}.log")
container: container:
None None
shell: shell:
""" """
ln -s {input.fastq} {output} ln -s {input.fastq} {output}
echo "{input.fastq} no gzipped. Symlink created in place of expected decompressed file." > {log} echo "{input.fastq} not gzipped. Symlink created in place of expected decompressed file." > {log}
""" """
rule trimSMRTbell: rule trimSMRTBellAdapters_hifi:
input: input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.smrtTrimmed.fastq"), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.smrtTrimmed.fastq"),
output: output:
outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.smrtTrimmed.fastq") outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.smrtTrimmed.fastq")
threads: threads:
resource['trimSMRTbell']['threads'] resource['trimSMRTBellAdapters_hifi']['threads']
resources: resources:
mem_mb=resource['trimSMRTbell']['mem_mb'], mem_mb=resource['trimSMRTBellAdapters_hifi']['mem_mb'],
time=resource['trimSMRTbell']['time'], time=resource['trimSMRTBellAdapters_hifi']['time'],
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}_trimSMRTbell.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/trimSMRTbell.{readCounter}.log")
priority: priority:
15 15
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
""" """
(cutadapt -j {threads} -o {output.outputFile} {input} -b ATCTCTCTCAACAACAACAACGGAGGAGGAGGAAAAGAGAGAGAT -b ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --discard-trimmed) &> {log} (cutadapt -j {threads} -o {output.outputFile} {input} -b AAAAAAAAAAAAAAAAAATTAACGGAGGAGGAGGA --overlap 35 -b ATCTCTCTCTTTTCCTCCTCCTCCGTTGTTGTTGTTGAGAGAGAT --overlap 45 --revcomp -e 0.1 --discard-trimmed) &> {log}
""" """
rule symlinkfornotSmartTrimmed: rule symlink_noSMRTBellAdaptTrim_hifi:
input: input:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"), os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
output: output:
...@@ -87,7 +89,7 @@ rule symlinkfornotSmartTrimmed: ...@@ -87,7 +89,7 @@ rule symlinkfornotSmartTrimmed:
ln -s {input} {output.outputFile} ln -s {input} {output.outputFile}
""" """
rule fastqc_hifi: rule fastQC_hifi:
input: input:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq") os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params: params:
...@@ -95,20 +97,20 @@ rule fastqc_hifi: ...@@ -95,20 +97,20 @@ rule fastqc_hifi:
output: output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html") os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html")
threads: threads:
resource['trimSMRTbell']['threads'] resource['fastQC_hifi']['threads']
resources: resources:
mem_mb=resource['fastqc_hifi']['mem_mb'], mem_mb=resource['fastQC_hifi']['mem_mb'],
time=resource['fastqc_hifi']['time'], time=resource['fastQC_hifi']['time'],
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}.{smrtornot}.FastQC.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/fastQC.hifi.{readCounter}.{smrtornot}.log")
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
""" """
(fastqc {input} -o {params.folder2out} -t {threads}) &> {log} (fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
""" """
rule multiqc_hifi: rule multiQC_hifi:
input: input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], smrtornot=dictSamples[wildcards.sample][1]) lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], smrtornot=dictSamples[wildcards.sample][1])
params: params:
...@@ -118,37 +120,37 @@ rule multiqc_hifi: ...@@ -118,37 +120,37 @@ rule multiqc_hifi:
output: output:
os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html") os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html")
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.multiqc.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/multiQC.{sample}.log")
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
"(multiqc {params.folder2qc} -o {params.folder2OUT} -n {params.filename}) &> {log}" "(multiqc {params.folder2qc} -o {params.folder2OUT} -n {params.filename}) &> {log}"
rule meryl_hifi_count: rule merylCount_hifi:
input: input:
reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq") reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params: params:
kmer = "{kmer}" kmer = "{kmer}"
threads: threads:
resource['meryl_hifi_count']['threads'] resource['merylCount_hifi']['threads']
resources: resources:
mem_mb=resource['meryl_hifi_count']['mem_mb'], mem_mb=resource['merylCount_hifi']['mem_mb'],
time=resource['meryl_hifi_count']['time'], time=resource['merylCount_hifi']['time'],
output: output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))), temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/meryl_hifi_count.{readCounter}.{kmer}.{smrtornot}.log")
priority: priority:
10 10
conda: conda:
os.path.join(workflow.basedir, "envs/merylMerq_2.yaml") os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell: shell:
""" """
(meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log} (meryl count k={params.kmer} threads={threads} {input.reads} output {output}) &> {log}
""" """
rule meryl_hifi_build: rule merylUnion_hifi:
input: input:
lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], kmer=dictSamples[wildcards.sample][0], smrtornot=dictSamples[wildcards.sample][1]) lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=dictReadCounter[wildcards.sample], kmer=dictSamples[wildcards.sample][0], smrtornot=dictSamples[wildcards.sample][1])
params: params:
...@@ -156,18 +158,18 @@ rule meryl_hifi_build: ...@@ -156,18 +158,18 @@ rule meryl_hifi_build:
removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/"), removeReadDIR_trimmed=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/"),
removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/") removeReadDIR_unzipped=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/")
threads: threads:
resource['meryl_hifi_build']['threads'] resource['merylUnion_hifi']['threads']
resources: resources:
mem_mb=resource['meryl_hifi_build']['mem_mb'], mem_mb=resource['merylUnion_hifi']['mem_mb'],
time=resource['meryl_hifi_build']['time'], time=resource['merylUnion_hifi']['time'],
output: output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl")), directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl")),
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.meryl_hifi.{kmer}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/meryl_hifi_combine.{sample}.{kmer}.log")
priority: priority:
10 10
conda: conda:
os.path.join(workflow.basedir, "envs/merylMerq_2.yaml") os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell: shell:
""" """
(meryl union-sum {input} output {output}) &> {log} (meryl union-sum {input} output {output}) &> {log}
......
rules/build_illumina.smk
+ 55
− 49
View file @ a98a21e5
...@@ -2,7 +2,13 @@ ...@@ -2,7 +2,13 @@
localrules: symlinkUnzippedFastq_R1, symlinkUnzippedFastq_R2, symLink_trim10xbarcodes_notrimAdapt, symlinks_no10xwithAdaptTrim, symlinks_no10xOrAdaptTrim, symlink_trim10xbarcodesR2, multiqc_hifi localrules: symlink_UnzippedFastq_R1_illumina,\
symlink_UnzippedFastq_R2_illumina, \
symLink_Trim10xBarcodes_noSequencingAdaptTrim_illumina, \
symlink_No10xWithSequencingAdaptTrim_illumina, \
symlink_No10xOrSequencingAdaptTrim_illumina, \
symlink_Trim10xBarcodes_R2_illumina, \
multiQC_illumina
...@@ -19,7 +25,7 @@ def R2_gzipped(wildcards): ...@@ -19,7 +25,7 @@ def R2_gzipped(wildcards):
def R2_notgzipped(wildcards): def R2_notgzipped(wildcards):
return noGzip_R2.loc[(wildcards.sample, wildcards.readCounter), "Library_R2"] return noGzip_R2.loc[(wildcards.sample, wildcards.readCounter), "Library_R2"]
rule unzipFastq_R1: rule unzipFastq_R1_illumina:
input: input:
assembly=R1_gzipped, assembly=R1_gzipped,
output: output:
...@@ -27,18 +33,18 @@ rule unzipFastq_R1: ...@@ -27,18 +33,18 @@ rule unzipFastq_R1:
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:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads: threads:
resource['unzipFastq_R1']['threads'] resource['unzipFastq_R1_illumina']['threads']
resources: resources:
mem_mb=resource['unzipFastq_R1']['mem_mb'], mem_mb=resource['unzipFastq_R1_illumina']['mem_mb'],
time=resource['unzipFastq_R1']['time'] time=resource['unzipFastq_R1_illumina']['time']
shell: shell:
""" """
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log} pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
""" """
rule symlinkUnzippedFastq_R1: rule symlink_UnzippedFastq_R1_illumina:
input: input:
assembly=R1_notgzipped, assembly=R1_notgzipped,
output: output:
...@@ -50,7 +56,7 @@ rule symlinkUnzippedFastq_R1: ...@@ -50,7 +56,7 @@ rule symlinkUnzippedFastq_R1:
ln -s {input} {output} ln -s {input} {output}
""" """
rule unzipFastq_R2: rule unzipFastq_R2_illumina:
input: input:
assembly=R2_gzipped, assembly=R2_gzipped,
output: output:
...@@ -58,18 +64,18 @@ rule unzipFastq_R2: ...@@ -58,18 +64,18 @@ rule unzipFastq_R2:
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:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
threads: threads:
resource['unzipFastq_R2']['threads'] resource['unzipFastq_R2_illumina']['threads']
resources: resources:
mem_mb=resource['unzipFastq_R2']['mem_mb'], mem_mb=resource['unzipFastq_R2_illumina']['mem_mb'],
time=resource['unzipFastq_R2']['time'] time=resource['unzipFastq_R2_illumina']['time']
shell: shell:
""" """
pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log} pigz -p {threads} -c -d -k {input.assembly} > {output} 2> {log}
""" """
rule symlinkUnzippedFastq_R2: rule symlink_UnzippedFastq_R2_illumina:
input: input:
assembly=R2_notgzipped, assembly=R2_notgzipped,
output: output:
...@@ -82,27 +88,27 @@ rule symlinkUnzippedFastq_R2: ...@@ -82,27 +88,27 @@ rule symlinkUnzippedFastq_R2:
""" """
rule trim10xbarcodes: rule trim10xBarcodes_illumina:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_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/temp_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_illumina']['threads']
resources: resources:
mem_mb=resource['trim10xbarcodes']['mem_mb'], mem_mb=resource['trim10xBarcodes_illumina']['mem_mb'],
time=resource['trim10xbarcodes']['time'] time=resource['trim10xBarcodes_illumina']['time']
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.10xTrimmed.10BarcodeRemoval_Trimmomatic.{trimAdapters}.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.10xTrimmed.10BarcodeRemoval_Trimmomatic.{trimAdapters}.log")
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
""" """
(trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log} (trimmomatic SE -threads {threads} {input.read1} {output.read1} HEADCROP:23) &> {log}
""" """
rule symlink_trim10xbarcodesR2: rule symlink_Trim10xBarcodes_R2_illumina:
input: input:
read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_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:
...@@ -116,7 +122,7 @@ rule symlink_trim10xbarcodesR2: ...@@ -116,7 +122,7 @@ rule symlink_trim10xbarcodesR2:
rule symLink_trim10xbarcodes_notrimAdapt: rule symLink_Trim10xBarcodes_noSequencingAdaptTrim_illumina:
input: input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"), read2=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.10xTrimmed.notAdaptTrimmed_Read2.fastq"),
...@@ -131,7 +137,7 @@ rule symLink_trim10xbarcodes_notrimAdapt: ...@@ -131,7 +137,7 @@ rule symLink_trim10xbarcodes_notrimAdapt:
ln -s {input.read2} {output.read2} ln -s {input.read2} {output.read2}
""" """
rule symlinks_no10xOrAdaptTrim: rule symlink_No10xOrSequencingAdaptTrim_illumina:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_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/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq") read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.notAdaptTrimmed_R2.fastq")
...@@ -146,7 +152,7 @@ rule symlinks_no10xOrAdaptTrim: ...@@ -146,7 +152,7 @@ rule symlinks_no10xOrAdaptTrim:
ln -s {input.read2} {output.read2} ln -s {input.read2} {output.read2}
""" """
rule symlinks_no10xwithAdaptTrim: rule symlink_No10xWithSequencingAdaptTrim_illumina:
input: input:
read1=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_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/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq") read2=os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/temp_unzipFastqs/{readCounter}.not10xTrimmed.AdaptTrimmed_R2.fastq")
...@@ -161,7 +167,7 @@ rule symlinks_no10xwithAdaptTrim: ...@@ -161,7 +167,7 @@ rule symlinks_no10xwithAdaptTrim:
ln -s {input.read2} {output.read2} ln -s {input.read2} {output.read2}
""" """
rule trimAdapters: rule trimSequencingAdapters_illumina:
input: input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"), read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_trimReads/{readCounter}.{trim10x}.AdaptTrimmed_Read2.fastq"),
...@@ -172,20 +178,20 @@ rule trimAdapters: ...@@ -172,20 +178,20 @@ rule trimAdapters:
read1=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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/temp_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['trimSequencingAdapters_illumina']['threads']
resources: resources:
mem_mb=resource['trimAdapters']['mem_mb'], mem_mb=resource['trimSequencingAdapters_illumina']['mem_mb'],
time=resource['trimAdapters']['time'], time=resource['trimSequencingAdapters_illumina']['time'],
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.AdaptTrimmed_tGalore.log") os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{readCounter}.{trim10x}.AdaptTrimmed_tGalore.log")
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
""" """
(trim_galore -j {threads} --basename {params.r1_prefix} --dont_gzip --length 65 -o {params.outputDir} --paired {input.read1} {input.read2}) &> {log} (trim_galore -j {threads} --basename {params.r1_prefix} --dont_gzip --length 65 -o {params.outputDir} --paired {input.read1} {input.read2}) &> {log}
""" """
rule fastqc_Illumina: rule fastQC_illumina:
input: input:
read1=os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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/temp_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")
...@@ -197,16 +203,16 @@ rule fastqc_Illumina: ...@@ -197,16 +203,16 @@ rule fastqc_Illumina:
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:
resource['fastqc_Illumina']['threads'] resource['fastQC_illumina']['threads']
resources: resources:
mem_mb=resource['fastqc_Illumina']['mem_mb'], mem_mb=resource['fastQC_illumina']['mem_mb'],
time=resource['fastqc_Illumina']['time'], time=resource['fastQC_illumina']['time'],
conda: conda:
os.path.join(workflow.basedir, "envs/pigz.yaml") os.path.join(workflow.basedir, "envs/UNZIP_and_QC.yaml")
shell: shell:
"(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}" "(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}"
rule multiqc_hifi: rule multiQC_illumina:
input: input:
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]), 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]) 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])
...@@ -219,22 +225,22 @@ rule multiqc_hifi: ...@@ -219,22 +225,22 @@ rule multiqc_hifi:
log: log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/logs/{sample}.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/UNZIP_and_QC.yaml")
shell: shell:
"(multiqc {params.folder2qc} -o {params.folder2out} -n {params.filename}) &> {log}" "(multiqc {params.folder2qc} -o {params.folder2out} -n {params.filename}) &> {log}"
rule meryl_R1: rule merylCount_R1_illumina:
input: input:
read1= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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:
resource['meryl_R1']['threads'] resource['merylCount_R1_illumina']['threads']
resources: resources:
mem_mb=resource['meryl_R1']['mem_mb'], mem_mb=resource['merylCount_R1_illumina']['mem_mb'],
time=resource['meryl_R1']['time'], time=resource['merylCount_R1_illumina']['time'],
output: output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/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:
...@@ -242,23 +248,23 @@ rule meryl_R1: ...@@ -242,23 +248,23 @@ rule meryl_R1:
priority: priority:
10 10
conda: conda:
os.path.join(workflow.basedir, "envs/merylMerq_2.yaml") os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell: shell:
""" """
export OMP_NUM_THREADS={threads} export OMP_NUM_THREADS={threads}
(meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log} (meryl count k={params.kmer} threads={threads} {input.read1} output {output}) &> {log}
""" """
rule meryl_R2: rule merylCount_R2_illumina:
input: input:
read2= os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/temp_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:
resource['meryl_R2']['threads'] resource['merylCount_R2_illumina']['threads']
resources: resources:
mem_mb=resource['meryl_R2']['mem_mb'], mem_mb=resource['merylCount_R2_illumina']['mem_mb'],
time=resource['meryl_R2']['time'], time=resource['merylCount_R2_illumina']['time'],
output: output:
temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/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:
...@@ -266,7 +272,7 @@ rule meryl_R2: ...@@ -266,7 +272,7 @@ rule meryl_R2:
priority: priority:
10 10
conda: conda:
os.path.join(workflow.basedir, "envs/merylMerq_2.yaml") os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell: shell:
""" """
export OMP_NUM_THREADS={threads} export OMP_NUM_THREADS={threads}
...@@ -274,7 +280,7 @@ rule meryl_R2: ...@@ -274,7 +280,7 @@ rule meryl_R2:
""" """
rule meryl_illumina_build: rule merylUnion_illumina:
input: input:
# 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]), # 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]), # 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]),
...@@ -286,10 +292,10 @@ rule meryl_illumina_build: ...@@ -286,10 +292,10 @@ rule meryl_illumina_build:
kmer = "{kmer}", kmer = "{kmer}",
path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/") path= os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/")
threads: threads:
resource['meryl_illumina_build']['threads'] resource['merylUnion_illumina']['threads']
resources: resources:
mem_mb=resource['meryl_illumina_build']['mem_mb'], mem_mb=resource['merylUnion_illumina']['mem_mb'],
time=resource['meryl_illumina_build']['time'], time=resource['merylUnion_illumina']['time'],
output: output:
directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/complete_illumina.{sample}.{kmer}.meryl")), directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/merylDb/complete_illumina.{sample}.{kmer}.meryl")),
log: log:
...@@ -297,7 +303,7 @@ rule meryl_illumina_build: ...@@ -297,7 +303,7 @@ rule meryl_illumina_build:
priority: priority:
10 10
conda: conda:
os.path.join(workflow.basedir, "envs/merylMerq_2.yaml") os.path.join(workflow.basedir, "envs/MERYL_MERQURY.yaml")
shell: shell:
""" """
export OMP_NUM_THREADS={threads} export OMP_NUM_THREADS={threads}
......
rules/evaluate.smk
+ 128
− 125
View file @ a98a21e5
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