diff --git a/rules/build_hifi.smk b/rules/build_hifi.smk
index bc1ce1c5eb702c77417628dcdecc66f4ae3f0819..6c616e58a4e259e71088011e4524aa41c7fb7493 100644
--- a/rules/build_hifi.smk
+++ b/rules/build_hifi.smk
@@ -3,12 +3,12 @@ localrules: symlinkUnzippedHifi, symlinkfornotSmartTrimmed, multiqc_hifi
-def fq_to_trimSMRTbell(wildcards):
- return trimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
-
-
-def fq_to_notTrimSMRTbell(wildcards):
- return notrimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
+# def fq_to_trimSMRTbell(wildcards):
+# return trimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
+#
+#
+# def fq_to_notTrimSMRTbell(wildcards):
+# return notrimSMRTbell.loc[(wildcards.sample, wildcards.readCounter), "hifi_reads"]
def hifi_gzipped(wildcards):
@@ -24,7 +24,7 @@ rule unzipHifi:
input:
fastq=hifi_gzipped,
output:
- temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
conda:
@@ -43,7 +43,7 @@ rule symlinkUnzippedHifi:
input:
fastq=hifi_notgzipped,
output:
- temp(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.{smrtornot}.fastq")),
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.{smrtornot}.fastq"),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/logs/hifiReads/{readCounter}.{smrtornot}_pigzUnzip.log")
container:
@@ -56,9 +56,9 @@ rule symlinkUnzippedHifi:
rule trimSMRTbell:
input:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.smrtTrimmed.fastq"),
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.smrtTrimmed.fastq"),
output:
- outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.smrtTrimmed.fastq"))
+ outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.smrtTrimmed.fastq")
threads:
resource['trimSMRTbell']['threads']
resources:
@@ -77,9 +77,9 @@ rule trimSMRTbell:
rule symlinkfornotSmartTrimmed:
input:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/01_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/temp_unzipFastqs/{readCounter}.notsmrtTrimmed.fastq"),
output:
- outputFile=temp(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.notsmrtTrimmed.fastq"))
+ outputFile=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.notsmrtTrimmed.fastq")
container:
None
shell:
@@ -89,11 +89,11 @@ rule symlinkfornotSmartTrimmed:
rule fastqc_hifi:
input:
- os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.{smrtornot}.fastq")
+ os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params:
- folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/")
+ folder2out=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc")
output:
- os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html")
+ os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/{readCounter}.{smrtornot}_fastqc.html")
threads:
resource['trimSMRTbell']['threads']
resources:
@@ -105,29 +105,29 @@ rule fastqc_hifi:
os.path.join(workflow.basedir, "envs/pigz.yaml")
shell:
"""
- mkdir {params.folder2out}
(fastqc {input} -o {params.folder2out} -t {threads}) &> {log}
"""
rule multiqc_hifi:
input:
- lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{readCounter}.{smrtornot}_fastqc.html"), sample=wildcards.sample, readCounter=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:
- folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/"),
- filename="{sample}.{smrtornot}.multiqcReport.html"
+ folder2qc=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/fastqc/"),
+ folder2OUT=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/"),
+ filename="{sample}.multiqcReport.html"
output:
- os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html")
+ os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/QC/multiqc/{sample}.multiqcReport.html")
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.{smrtornot}.multiqc.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.multiqc.log")
conda:
os.path.join(workflow.basedir, "envs/pigz.yaml")
shell:
- "(multiqc {params.folder2qc} -o {params.folder2qc} -n {params.filename}) &> {log}"
+ "(multiqc {params.folder2qc} -o {params.folder2OUT} -n {params.filename}) &> {log}"
rule meryl_hifi_count:
input:
- reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/02_trimReads/{readCounter}.{smrtornot}.fastq")
+ reads=os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/temp_trimReads/{readCounter}.{smrtornot}.fastq")
params:
kmer = "{kmer}"
threads:
@@ -136,7 +136,7 @@ rule meryl_hifi_count:
mem_mb=resource['meryl_hifi_count']['mem_mb'],
time=resource['meryl_hifi_count']['time'],
output:
- temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))),
+ temp(directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/" + "{readCounter}" + "_hifi_dB.{smrtornot}.{kmer}.meryl"))),
log:
os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{readCounter}_hifi_{kmer}.{smrtornot}.log")
priority:
@@ -150,18 +150,20 @@ rule meryl_hifi_count:
rule meryl_hifi_build:
input:
- lambda wildcards: expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/{readCounter}_hifi_dB.{smrtornot}.{kmer}.meryl/"), sample=wildcards.sample, readCounter=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:
- kmer = "{kmer}"
+ kmer = "{kmer}",
+ 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/")
threads:
resource['meryl_hifi_build']['threads']
resources:
mem_mb=resource['meryl_hifi_build']['mem_mb'],
time=resource['meryl_hifi_build']['time'],
output:
- directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl")),
+ directory(os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/merylDb/complete_hifi.{sample}.{kmer}.meryl")),
log:
- os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}_hifi_{smrtornot}.{kmer}.log")
+ os.path.join(config['Results'], "0_buildDatabases/{sample}/hifiReads/logs/{sample}.meryl_hifi.{kmer}.log")
priority:
10
conda:
@@ -169,4 +171,6 @@ rule meryl_hifi_build:
shell:
"""
(meryl union-sum {input} output {output}) &> {log}
+ rm -r {params.removeReadDIR_trimmed}
+ rm -r {params.removeReadDIR_unzipped}
"""