Update upstream source from tag 'upstream/0.4.25'

Update to upstream version '0.4.25'
with Debian dir ef38550465f3cf1d76cf99637c633405deac509c

3 files changed, 22 insertions, 1 deletions

diff --git a/HISTORY.md b/HISTORY.md
index a695984..b52dfbc 100644
--- a/HISTORY.md
+++ b/HISTORY.md
@@ -1,3 +1,7 @@
+0.4.25
+
+* [fix outliers samples](https://github.com/nf-core/smrnaseq/issues/137). When there is no identification of reference sequences or isomirs, the multiqc module will fails because it won't find the expected keys. Adding 0 when is the case.
+
 0.4.24
 
 * [fix bad](https://github.com/miRTop/mirtop/issues/64) annotation when 5 or more T/A at the end of the sequence by @DrHogart
diff --git a/mirtop/gff/stats.py b/mirtop/gff/stats.py
index ad3e7fe..d1d3c94 100644
--- a/mirtop/gff/stats.py
+++ b/mirtop/gff/stats.py
@@ -103,6 +103,20 @@ def _classify(srna_type, attr, samples):
     return lines
 
 
+def _add_missing(df):
+    # ref_miRNA_mean
+    category = "ref_miRNA_mean"
+    if sum(df['category']==category) == 0:
+        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
+        df = df.append(df2, ignore_index = True)
+    
+    category = "isomiR_sum"
+    if sum(df['category']==category) == 0:
+        df2 = {'category': category, 'sample': df['sample'].iat[0], 'counts': 0}
+        df = df.append(df2, ignore_index = True)
+    
+    return df
+
 def _summary(lines):
     """
     Summarize long table according to thresholds
@@ -113,10 +127,13 @@ def _summary(lines):
     df.counts = df.counts.astype(int)
     df_sum = df.groupby(['category', 'sample'], as_index=False).sum()
     df_sum['category'] = ["%s_sum" % r for r in df_sum['category']]
+    df_sum = _add_missing(df_sum)
     df_count = df.groupby(['category', 'sample'], as_index=False).count()
     df_count['category'] = ["%s_count" % r for r in df_count['category']]
+    df_count = _add_missing(df_count)
     df_mean = df.groupby(['category', 'sample'], as_index=False).mean()
     df_mean['category'] = ["%s_mean" % r for r in df_mean['category']]
+    df_mean = _add_missing(df_mean)
     df = pd.concat([df_sum, df_count, df_mean])
     return df
 
diff --git a/setup.py b/setup.py
index 7ee2b42..596a3e3 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = '0.4.24'
+version = '0.4.25'
 
 url = 'http://github.com/mirtop/mirtop'