Update by asebastian on Mon Oct 16 14:29:50 EDT 2017 from Aswathys-iMac.local
@@ -104,11 +104,11 @@ trim_primer: fastqc
trim_quality: trim_primer
mkdir -p $(QTRIM_DIR)/logs
- cat $(UPDATED_SAMPLE_INFO) |parallel --verbose --progress -j $(THREADS) --header : --colsep '\t' 'bbduk.sh \
+ cat $(UPDATED_SAMPLE_INFO) |parallel --verbose --progress -j $(THREADS) --header : --colsep '\t' bbduk.sh \
in1=$(PTRIM_DIR)/{sample_name}_R1_trimp.fq.gz in2=$(PTRIM_DIR)/{sample_name}_R2_trimp.fq.gz \
qtrim=rl trimq=$(TRIM_QUALITY) minlength=35 overwrite=true \
out1=$(QTRIM_DIR)/{sample_name}_R1_trim.fq.gz \
- out2=$(QTRIM_DIR)/{sample_name}_R2_trim.fq.gz 2>$(QTRIM_DIR)/logs/{sample_name}_stats.txt'
+ out2=$(QTRIM_DIR)/{sample_name}_R2_trim.fq.gz stats=$(QTRIM_DIR)/logs/{sample_name}_stats.txt
cat $(QTRIM_DIR)/logs/*stats.txt > $(RESULT_DIR)/trimq_stats.txt
#
# quality report
