Update by asebastian on Thu Oct 19 12:51:22 EDT 2017 from Aswathys-iMac.local
INPUT_DATA = {{data.value}}
INPUT_SAMPLE_INFO = {{sampleinfo.value}}
TRIM_QUALITY={{trim_quality.value}}
+TRIM_PRIMER ={{ trim_primer.value }}
THREADS ={{ threads.value}}
#
@@ -17,8 +18,11 @@ QTRIM_DIR = $(ANALYSIS_DIR)/trim/trimq
UPDATED_SAMPLE_INFO = updated_sampleinfo.txt
-#all: trim_quality
-# @echo "executes all commands"
+all : trim_primer trim_quality
+
+all: trim_primer
+
+all : trim_quality
extract:
#
@@ -71,7 +75,7 @@ multiqc: fastqc $(RESULT_DIR)
#
-trim_primer: $(RESULT_DIR)
+trim_primer: $(RESULT_DIR) updated_sample_info
echo "trimming primer"
#
mkdir -p $(PTRIM_DIR)/logs
@@ -103,7 +107,7 @@ R1={sample_name}_R1_trimp.fq.gz
R2={sample_name}_R2_trimp.fq.gz
endif
-trim_quality: trim_quality != None
+trim_quality: $(RESULT_DIR) updated_sample_info
echo $(INDIR),$(R1)
cat $(UPDATED_SAMPLE_INFO) |parallel --verbose --progress -j $(THREADS) --header : --colsep '\t' bbduk.sh \
in1=$(INDIR)/$(R1) in2=$(INDIR)/$(R2) \
