incorrect Snakefile in previous push

Snakefile

@@ -63,8 +63,8 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri
 	samples['AdpaterTrimorNot'] = np.where(samples['trimAdapters'] == "True", "AdaptTrimmed", "notAdaptTrimmed")
 	for i in samples['sample'].unique():
 		d10xtrim[i] = [samples['10xtrimorNot'][j] for j in samples[samples['sample']==i].index]
-	testDict=samples[['sample','meryl_kmer_size', '10xtrimorNot','AdpaterTrimorNot']]
-	testDict=testDict.set_index(['sample']).T.to_dict('list')
+	dictSamples=samples[['sample','meryl_kmer_size', '10xtrimorNot','AdpaterTrimorNot']]
+	dictSamples=dictSamples.set_index(['sample']).T.to_dict('list')
 
 	testDictQC=samples[['sample', '10xtrimorNot', 'AdpaterTrimorNot', 'fastQC']]
 	testDictQC = testDictQC[testDictQC['fastQC'] == "True"]
@@ -80,9 +80,9 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri
 	drunQCtrim = {}
 	for i in runQC['sample'].unique():
 		drunQCtrim[i] = [runQC['readCounter'][j] for j in runQC[runQC['sample']==i].index]
-	d = {}
+	dictReadCounter = {}
 	for i in samples['sample'].unique():
-		d[i] = [samples['readCounter'][j] for j in samples[samples['sample']==i].index]
+		dictReadCounter[i] = [samples['readCounter'][j] for j in samples[samples['sample']==i].index]
 	dkmerSize = {}
 	samples['gzipped_R1']=samples['Library_R1'].apply(gzipped_or_not)
 	samples['gzipped_R2']=samples['Library_R2'].apply(gzipped_or_not)
@@ -109,9 +109,9 @@ if set(['sample', 'Library_R1', 'Library_R2', 'meryl_kmer_size', 'trim10X', 'tri
 	ruleAllQCFiles=[]
 	if samples['fastQC'].str.contains('True').any():
 		ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/illuminaReads/05_multiqc/{sample}.{trim10x}.{trimAdapters}.multiqcReport.html"), sample=key, trim10x=value1, trimAdapters=value2) for key, [value1, value2, value3] in testDictQC.items()]
-	ruleAll=[expand(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/complete_{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl"), sample=key, kmer=value1, trim10x=value2, trimAdapters=value3) for key, [value1, value2, value3] in testDict.items()]
+	ruleAll=[expand(os.path.join(config['Results'], "0_buildDatabases/{sample}/illuminaReads/03_merylDb/complete_{sample}_illuminaDb.{trim10x}.{trimAdapters}.{kmer}.meryl"), sample=key, kmer=value1, trim10x=value2, trimAdapters=value3) for key, [value1, value2, value3] in dictSamples.items()]
 
-elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).issubset(samples.columns):
+elif set(['sample', 'hifi_reads', 'meryl_kmer_size','trimSMRTbell', 'fastQC']).issubset(samples.columns):
 	whichRule = "rules/build_hifi.smk"
 	samples=samples.reset_index()
 	samples['readCounter'] = samples.groupby(['sample']).cumcount()+1
@@ -121,8 +121,8 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).
 	samplesDict=samples.set_index('sample').T.to_dict('list')
 
 	samples=samples.reset_index()
-	testDict=samples[['sample','meryl_kmer_size', 'smrtornot']]
-	testDict=testDict.set_index(['sample']).T.to_dict('list')
+	dictSamples=samples[['sample','meryl_kmer_size', 'smrtornot']]
+	dictSamples=dictSamples.set_index(['sample']).T.to_dict('list')
 
 
 	testDictQC=samples[['sample', 'smrtornot', 'fastQC']]
@@ -161,9 +161,9 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).
 	dkmerDups=samples.drop_duplicates('meryl_kmer_size', keep='first')
 	for i in samples['sample'].unique():
 		dkmerSize[i] = [dkmerDups['meryl_kmer_size'][j] for j in dkmerDups[dkmerDups['sample']==i].index]
-	d = {}
+	dictReadCounter = {}
 	for i in samples['sample'].unique():
-		d[i] = [samples['readCounter'][j] for j in samples[samples['sample']==i].index]
+		dictReadCounter[i] = [samples['readCounter'][j] for j in samples[samples['sample']==i].index]
 	samples['gzipped_hifi']=samples['hifi_reads'].apply(gzipped_or_not)
 
 
@@ -180,7 +180,7 @@ elif set(['sample', 'hifi_reads', 'meryl_kmer_size'	,'trimSMRTbell', 'fastQC']).
 
 	if samples['fastQC'].str.contains('True').any():
 		ruleAllQCFiles=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/05_multiqc/{sample}.{smrtornot}.multiqcReport.html"), sample=key, smrtornot=value1) for key, [value1, value2] in testDictQC.items()]
-	ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in testDict.items()]
+	ruleAll=[expand(os.path.join(config['Results'],"0_buildDatabases/{sample}/hifiReads/03_merylDb/complete_hifi_{sample}_dB.{smrtornot}.{kmer}.meryl"), sample=key, kmer=value1, smrtornot=value2) for key, [value1, value2] in dictSamples.items()]
 elif set(['ID',	'PRI_asm', 'ALT_asm',	'merylDB',	'merylDB_kmer', 'genomeSize', 'HiC_R1', 'HiC_R2']).issubset(samples.columns):
 	whichRule = "rules/evaluate.smk"
 	samples['genomeSize']=samples['genomeSize'].apply(genomeSize_auto_or_not)
@@ -239,7 +239,7 @@ elif set(['ID',	'PRI_asm', 'ALT_asm',	'merylDB',	'merylDB_kmer', 'genomeSize', '
 	testDict=samples.T.to_dict('list')
 
 	ruleAllQCFiles=[]
-	ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_aggregatedResults.tsv"), asmID=list(testDict.keys())), os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv"), 	os.path.join(config['Results'],"1_evaluation/finalResults/FULL_Report_PDF.pdf"),os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
+	ruleAll=expand(os.path.join(config['Results'],"1_evaluation/{asmID}/06_keyResults/{asmID}_aggregatedResults.tsv"), asmID=list(dictSamples.keys())), os.path.join(config['Results'],"1_evaluation/finalResults/Combined_Results_FULLTABLE.tsv"), 	os.path.join(config['Results'],"1_evaluation/finalResults/FULL_Report_PDF.pdf"),os.path.join(config['Results'],"1_evaluation/finalResults/FULL_TABLE_PDF.pdf")
 
 else:
 	raise ValueError('Sample Sheet for not recognised. Please make sure you are using the correct sample sheet')