diff --git a/bin/ngseasy_trimmomatic b/bin/ngseasy_trimmomatic index f9df4ac..3503442 100755 --- a/bin/ngseasy_trimmomatic +++ b/bin/ngseasy_trimmomatic @@ -472,9 +472,6 @@ elif [[ "$TRIM" == "atrim" ]]; then ######################################################################################################## logger_ngseasy "[${NGSEASY_STEP}]:START qc of raw fastq files" ${LOGFILE} logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - adaptor trim. Adaptor and read quality trimming" ${LOGFILE} - -## run trimmomatic -# logger_ngseasy "[${NGSEASY_STEP}]:[cmd]: ILLUMINACLIP:${adapter_fa}:2:30:10:5:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 AVGQUAL:2 MINLEN:75 " ${LOGFILE} ${DOCKER_RUN} \ @@ -517,7 +514,7 @@ logger_ngseasy "[${NGSEASY_STEP}]:FastQC post Trimmomatic" ${LOGFILE} ######################################################################################################## ## Just QC FASTQ NO ADAPTOR TRIM -# btrim is basic qc-trim +## btrim is basic qc-trim ######################################################################################################## elif [[ "$TRIM" == "btrim" ]]; then @@ -525,7 +522,7 @@ logger_ngseasy "[${NGSEASY_STEP}]:START qc of raw fastq files" ${LOGFILE} logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - basic trim. Just read quality trimming. No adaptor trimming" ${LOGFILE} ######################################################################################################## -## run trimmomatic +## run trimmomatic btrim ######################################################################################################## ${DOCKER_RUN} \ --rm=true \