Save SPAdes report and correct Trimmomatic option

Allways save SPAdes report;
Correct Trimmomatic -phred option parsing.

INNUca.py

@@ -257,7 +257,7 @@ def run_INNUca(sampleName, outdir, fastq_files, args, script_path, scheme):
 
 		# Run SPAdes
 		if not args.skipSPAdes:
-			run_successfully, pass_qc, time_taken, failing, contigs = spades.runSpades(sampleName, outdir, threads, fastq_files, args.spadesNotUseCareful, args.spadesMaxMemory, args.spadesMinCoverageAssembly, args.spadesMinContigsLength, genomeSize, args.spadesKmers, maximumReadsLength, args.spadesSaveReport, args.spadesDefaultKmers, args.spadesMinCoverageContigs)
+			run_successfully, pass_qc, time_taken, failing, contigs = spades.runSpades(sampleName, outdir, threads, fastq_files, args.spadesNotUseCareful, args.spadesMaxMemory, args.spadesMinCoverageAssembly, args.spadesMinContigsLength, genomeSize, args.spadesKmers, maximumReadsLength, args.spadesDefaultKmers, args.spadesMinCoverageContigs)
 			runs['SPAdes'] = [run_successfully, pass_qc, time_taken, failing]
 
 			if run_successfully:

README.md

@@ -56,8 +56,8 @@ Usage
                      [--spadesNotUseCareful] [--spadesMinContigsLength N]
                      [--spadesKmers 55 77 | --spadesDefaultKmers]
                      [--spadesMaxMemory N] [--spadesMinCoverageAssembly 10]
-                     [--spadesMinCoverageContigs N] [--spadesSaveReport]
-                     [--pilonKeepFiles] [--pilonKeepSPAdesAssembly]
+                     [--spadesMinCoverageContigs N] [--pilonKeepFiles]
+                     [--pilonKeepSPAdesAssembly]
 
     INNUca - Reads Control and Assembly
 
@@ -152,8 +152,6 @@ Usage
                             Minimum contigs coverage. After assembly only keep
                             contigs with reported coverage equal or above this
                             value (default: 5)
-      --spadesSaveReport    Tells INNUca to store the number of contigs and
-                            assembled nucleotides for each sample
     SPAdes k-mers options (one of the following):
       --spadesKmers 55,77   Manually sets SPAdes k-mers lengths (all values must
                             be odd, less than 128) (default: 55, 77, 99, 113,

modules/spades.py

@@ -71,7 +71,7 @@ def define_kmers(kmers, maximumReadsLength):
 
 # Run SPAdes procedure
 @spades_timer
-def runSpades(sampleName, outdir, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, minContigsLength, estimatedGenomeSizeMb, kmers, maximumReadsLength, saveReport, defaultKmers, minCoverageContigs):
+def runSpades(sampleName, outdir, threads, fastq_files, notUseCareful, maxMemory, minCoverageAssembly, minContigsLength, estimatedGenomeSizeMb, kmers, maximumReadsLength, defaultKmers, minCoverageContigs):
 	pass_qc = False
 	failing = {}
 	failing['sample'] = False
@@ -110,11 +110,10 @@ def runSpades(sampleName, outdir, threads, fastq_files, notUseCareful, maxMemory
 			if number_contigs == 0:
 				run_successfully = False
 
-		if saveReport:
-			report_file = os.path.join(outdir, 'spades_report.txt')
-			with open(report_file, 'wt') as writer:
-				writer.write('#contigs' + '\n' + str(number_contigs) + '\n' + '#bp' + '\n' + str(number_bases) + '\n')
-				writer.flush()
+		report_file = os.path.join(outdir, 'spades_report.txt')
+		with open(report_file, 'wt') as writer:
+			writer.write('#contigs' + '\n' + str(number_contigs) + '\n' + '#bp' + '\n' + str(number_bases) + '\n')
+			writer.flush()
 
 		if failing['sample'] is False:
 			if number_bases >= estimatedGenomeSizeMb * 1000000 * 0.8 and number_bases <= estimatedGenomeSizeMb * 1000000 * 1.5:

modules/trimmomatic.py

@@ -8,7 +8,7 @@ def trimmomatic(sampleName, trimmomatic_folder, threads, adaptersFasta, script_p
 	fastq = sorted(fastq_files)[0]
 
 	# Run Trimmomatic
-	command = ['trimmomatic-0.36.jar', 'PE', '-threads', str(threads), '-basein', fastq, '-baseout', os.path.join(trimmomatic_folder, str(sampleName + '.fastq.gz')), '', '', '', str('SLIDINGWINDOW:' + slidingWindow), str('LEADING:' + str(leading)), str('TRAILING:' + str(trailing)), str('MINLEN:' + str(minLength)), 'TOPHRED33']
+	command = ['trimmomatic-0.36.jar', 'PE', '-threads', str(threads), '-basein', fastq, '-baseout', os.path.join(trimmomatic_folder, str(sampleName + '.fastq.gz')), '', '', '', str('SLIDINGWINDOW:' + slidingWindow), str('LEADING:' + str(leading)), str('TRAILING:' + str(trailing)), str('MINLEN:' + str(minLength)), 'TOPHRED33', '']
 
 	if not doNotTrimCrops:
 		if maxReadsLength is not None:
@@ -47,11 +47,11 @@ def trimmomatic(sampleName, trimmomatic_folder, threads, adaptersFasta, script_p
 
 	if not run_successfully:
 		print 'Trimmomatic fail! Trying run with Phred+33 enconding defined...'
-		command.append('-phred33')
+		command[16] = '-phred33'
 		run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None)
 		if not run_successfully:
 			print 'Trimmomatic fail again! Trying run with Phred+64 enconding defined...'
-			command[18] = '-phred64'
+			command[16] = '-phred64'
 			run_successfully, stdout, stderr = utils.runCommandPopenCommunicate(command, False, None)
 
 	return run_successfully

modules/utils.py

@@ -53,7 +53,6 @@ def parseArguments(version):
 	spades_options.add_argument('--spadesMaxMemory', type=int, metavar='N', help='The maximum amount of RAM Gb for SPAdes to use', required=False, default=25)
 	spades_options.add_argument('--spadesMinCoverageAssembly', type=spades_cov_cutoff, metavar='10', help='The minimum number of reads to consider an edge in the de Bruijn graph (or path I am not sure). Can also be auto or off', required=False, default='off')
 	spades_options.add_argument('--spadesMinCoverageContigs', type=int, metavar='N', help='Minimum contigs coverage. After assembly only keep contigs with reported coverage equal or above this value', required=False, default=5)
-	spades_options.add_argument('--spadesSaveReport', action='store_true', help='Tells INNUca to store the number of contigs and assembled nucleotides for each sample')
 
 	spades_kmers_options = parser.add_mutually_exclusive_group()
 	spades_kmers_options.add_argument('--spadesKmers', nargs='+', type=int, metavar='55 77', help='Manually sets SPAdes k-mers lengths (all values must be odd, lower than 128)', required=False, default=[55, 77, 99, 113, 127])