1. Casey Dunn
  2. agalma

Commits

Casey Dunn  committed 3eeb866

pass argument through to filter_illumina, re #49

  • Participants
  • Parent commits 0de506c
  • Branches issue-49

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Files changed (1)

File agalma/sanitize.py

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 	default=28, help="""
 	Filter out reads that have a mean quality < MIN.""")
 	
-pipe.add_argument('number', short='n', type=int, metavar='NUM',
+pipe.add_argument('nreads', short='n', type=int, metavar='NUM',
 	default=None, help="""
 	Consider only the first NUM reads that pass filter, others are discarded""")
 
 		wrappers.FastQC(fastqc, outdir)
 
 @pipe.stage
-def sanitize(id, data, outdir, gzip, quality):
+def sanitize(id, data, outdir, gzip, quality, nreads):
 	"""Filter out low-quality and adapter-contaminated reads"""
 
 	outputs = []
 		outputs,
 		#outputs[:-1],
 		#unpaired_output=outputs[-1],
-		quality=quality, sep='/')
+		quality=quality, 
+		nreads = nreads,
+		sep='/')
 
 	data.append(outputs)
 	finish('data')