# HG changeset patch
# User pjbriggs
# Date 1539766917 14400
# Node ID 7b2c40450792b7ec8f1f12666d57137afb72fbcd
# Parent  e832be1635b4746257c58d84ae93ec405d31ee42
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 601f7d1e21b25c583cc6e1a563029bab3f226921-dirty

diff -r e832be1635b4 -r 7b2c40450792 amplicon_analysis_pipeline.py
--- a/amplicon_analysis_pipeline.py	Tue Oct 16 10:54:44 2018 -0400
+++ b/amplicon_analysis_pipeline.py	Wed Oct 17 05:01:57 2018 -0400
@@ -60,9 +60,10 @@
     sys.stderr.write("%s\n\n" % ('*'*width))
 
 def clean_up_name(sample):
-    # Remove trailing "_L[0-9]+_001" from Fastq
-    # pair names
-    split_name = sample.split('_')
+    # Remove extensions and trailing "_L[0-9]+_001" from
+    # Fastq pair names
+    sample_name = '.'.join(sample.split('.')[:1])
+    split_name = sample_name.split('_')
     if split_name[-1] == "001":
         split_name = split_name[:-1]
     if split_name[-1].startswith('L'):
@@ -152,6 +153,7 @@
         fastqs = iter(args.fastq_pairs)
         for sample_name,fqr1,fqr2 in zip(fastqs,fastqs,fastqs):
             sample_name = clean_up_name(sample_name)
+            print "Cleaned up sample name: %s" % sample_name
             r1 = "%s_R1_.fastq" % sample_name
             r2 = "%s_R2_.fastq" % sample_name
             os.symlink(fqr1,r1)