Discard reads without primers

Fix for #22
metagenlab · May 1, 2020 · 476c10e · 476c10e
1 parent fcb9b0a
commit 476c10e
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/rules/1_2_DADA2_ASVs/scripts/1_cutadapt.py b/rules/1_2_DADA2_ASVs/scripts/1_cutadapt.py
@@ -18,6 +18,7 @@
     -G '{snakemake.params[reverse_primer]}' \
     -A '{forward_primer_compl}' \
     --match-read-wildcards \
+    --discard-untrimmed \
     {snakemake.input[R1_raw_reads]} \
     {snakemake.input[R2_raw_reads]} >> {snakemake.log[0]}""")
 
@@ -33,6 +34,7 @@
     -g '{snakemake.params[forward_primer]}' \
     -G '{snakemake.params[reverse_primer]}' \
     --match-read-wildcards \
+    --discard-untrimmed \
     {snakemake.input[R1_raw_reads]} \
     {snakemake.input[R2_raw_reads]} >> {snakemake.log[0]}""")