# HG changeset patch
# User pjbriggs
# Date 1576574657 0
# Node ID 04e71fda5b9c9f696838e5ec1e79eda2dff40d9f
# Parent  1bc0077b2c91ecd794d82b3b68559129593b5df4
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 06b2cc0d518a6a4d77b865b6567e0bc6a2fb26df-dirty

diff -r 1bc0077b2c91 -r 04e71fda5b9c amplicon_analysis_pipeline.py
--- a/amplicon_analysis_pipeline.py	Tue Dec 17 09:12:13 2019 +0000
+++ b/amplicon_analysis_pipeline.py	Tue Dec 17 09:24:17 2019 +0000
@@ -277,6 +277,9 @@
 """)
         # Look for raw and trimmed FastQC output for each sample
         for sample_name in sample_names:
+            # Replace underscores with hyphens in sample names
+            sample_name = sample_name.replace('_','-')
+            # Write HTML file with links to the FastQC boxplots
             fastqc_dir = os.path.join(sample_name,"FastQC")
             quality_boxplots.write("<h2>%s</h2>" % sample_name)
             for d in ("Raw","cutdapt_sickle/Q%s" % phred_score):
@@ -300,7 +303,6 @@
                     if boxplot is None:
                         boxplot = "Missing plot"
                     quality_boxplots.write("<h4>%s</h4><p>%s</p>" %
-
                                            (os.path.basename(f),
                                             boxplot))
             quality_boxplots.write("""</body>