Merge branch 'master' of gitlab.pasteur.fr:bli/bioinfo_utils

small_RNA-seq/small_RNA-seq.snakefile

@@ -218,7 +218,7 @@ def sum_dataframes(dfs):
 
 def sum_counts(fname):
     p = Popen(
-        ['awk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
+        ['awk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
         stdout=PIPE,
         stderr=PIPE)
     result, err = p.communicate()