silence the echo statements

workflow/scripts/remove_low_complexity_grep.sh

@@ -5,21 +5,21 @@ set +e
 #read1="${snakemake_input[read1]}"
 read1="${snakemake_input[reads]}"
 #read2="${snakemake_input[read2]}"
-echo $reads
+#echo $reads
 
 ids="${snakemake_input[ids]}"
 out1="${snakemake_output}"
 log_fp="$(dirname "${ids}")"
 base_name="$(basename "${read1}")"
 SAMPLEID=${base_name%.fastq.gz}
 
-echo "make list of trimmomatic output IDs"
+#echo "make list of trimmomatic output IDs"
 zgrep "^@" $read1 > ${log_fp}/${SAMPLEID}.trimm_verbose_ids
 sed 's/ .*$//g' ${log_fp}/${SAMPLEID}.trimm_verbose_ids | sed 's/\/[1-2]$//g' | sort -u > ${log_fp}/${SAMPLEID}.trimm_ids
 sed 's/ .*$//g' ${ids} | sed 's/\/[1-2]$//g' | sort -u > ${ids}_unique
-echo "grep -v the komplexity ids to get subsample to keep"
+#echo "grep -v the komplexity ids to get subsample to keep"
 grep -v -f ${ids}_unique ${log_fp}/${SAMPLEID}.trimm_ids > ${log_fp}/${SAMPLEID}.komplexity_keep_ids
-echo "filter reads with zgrep"
+#echo "filter reads with zgrep"
 komp_fp="$(dirname "${out1}")"
 mkdir -p $komp_fp &>/dev/null # be silent
 zgrep -A 3 -f ${log_fp}/${SAMPLEID}.komplexity_keep_ids $read1 | sed '/^--$/d' | gzip > $out1
@@ -30,17 +30,17 @@ newheaders=$( zgrep -c "^@" $out1 )
 newlines=$( zcat $out1 | wc -l )
 numids=$(< ${log_fp}/${SAMPLEID}.komplexity_keep_ids wc -l )
 explines=$(( "$numids" + "$numids" + "$numids" + "$numids" ))
-echo $newheaders
-echo $newlines
-echo $explines
-echo $numids
+#echo $newheaders
+#echo $newlines
+#echo $explines
+#echo $numids
 if [ "$newheaders" -eq "$numids" ]; then
 	if [ "$newlines" -eq "$explines" ]; then
 		continue
 	fi
 else	
 	exitcode=$(( "$exitcode" + 1 ))	
-	echo "Your filtered read 1 file does not equal the expected length"
+	#echo "Your filtered read 1 file does not equal the expected length"
 fi
 
 if [ $exitcode -eq 1 ]