Missing explicit handling of rRNA.

small_RNA-seq/small_RNA-seq.snakefile

@@ -552,7 +552,7 @@ def sum_counts(fname):
     p = Popen(
         # ['awk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
         # slightly faster
-        ['mawk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
+        ['mawk', '$1 ~ /^piRNA$|^miRNA$|^pseudogene$|^satellites_rmsk$|^simple_repeats_rmsk$|^rRNA$|^protein_coding_|^.NA_transposons_rmsk$/ {sum += $2} END {print sum}', fname],
         stdout=PIPE,
         stderr=PIPE)
     (result, err) = p.communicate()
@@ -1828,6 +1828,10 @@ rule gather_small_RNA_counts:
                     *{f"simrep_si_{suffix}" for suffix in SI_SUFFIXES},
                     *{f"simrep_siu_{suffix}" for suffix in SI_SUFFIXES}}:
                 drop = ["simple_repeats_rmsk"]
+            elif wildcards.small_type in {
+                    *{f"ri_si_{suffix}" for suffix in SI_SUFFIXES},
+                    *{f"ri_siu_{suffix}" for suffix in SI_SUFFIXES}}:
+                drop = ["rRNA"]
             elif wildcards.small_type in {
                     *{f"all_si_{suffix}" for suffix in SI_SUFFIXES},
                     *{f"all_siu_{suffix}" for suffix in SI_SUFFIXES}}: