diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile index caf561c02e1890d6db5bd47df9f543bd4e09851e..26f297c08acb75d9971cca8239040721dcc6bce8 100644 --- a/small_RNA-seq/small_RNA-seq.snakefile +++ b/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()