build hifi changes

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}
 		"""