dictionary mis-named

rules/build_illumina.smk

@@ -208,8 +208,8 @@ 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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[wildcards.sample][2])
+		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])
 	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/"),
@@ -276,10 +276,10 @@ 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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], trimAdapters=testDict[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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], kmer=testDict[wildcards.sample][0], trimAdapters=testDict[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=d[wildcards.sample], trim10x=testDict[wildcards.sample][1], kmer=testDict[wildcards.sample][0], trimAdapters=testDict[wildcards.sample][2])
+		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])
 	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/"),