diff --git a/bin/ngseasy_trimmomatic b/bin/ngseasy_trimmomatic index b3cfd4a..f9df4ac 100755 --- a/bin/ngseasy_trimmomatic +++ b/bin/ngseasy_trimmomatic @@ -477,24 +477,23 @@ logger_ngseasy "[${NGSEASY_STEP}]:TRIM set to [$TRIM] - adaptor trim. Adaptor an # 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} \ - --rm=true \ - -v ${PROJECT_DIR}:/home/pipeman/ngs_projects \ - -v ${NGSResources}:/home/pipeman/ngs_resources \ - --name trimmomatic_${BAM_PREFIX} \ - -t compbio/ngseasy-trimmomatic:${NGSEASYVERSION} java -XX:ParallelGCThreads=1 -jar /usr/local/pipeline/Trimmomatic-0.32/trimmomatic-0.32.jar \ - PE \ - -threads ${NCPU} \ - ${SOUTDocker}/fastq/${FQ1} \ - ${SOUTDocker}/fastq/${FQ2} \ - ${qcPEFQ1} ${qcSEFQ1} \ - ${qcPEFQ2} ${qcSEFQ2} \ - ILLUMINACLIP:${adapter_fa}:2:30:10:5:true \ - LEADING:3 \ - TRAILING:3 \ - SLIDINGWINDOW:4:15 \ - AVGQUAL:2 \ - MINLEN:75 +${DOCKER_RUN} \ + --rm=true \ + -v ${PROJECT_DIR}:/home/pipeman/ngs_projects \ + --name trimmomatic_${BAM_PREFIX} \ + -t compbio/ngseasy-trimmomatic:${NGSEASYVERSION} java -XX:ParallelGCThreads=1 -jar /usr/local/pipeline/Trimmomatic-0.32/trimmomatic-0.32.jar \ + PE \ + -threads ${NCPU} \ + ${SOUTDocker}/fastq/${FQ1} \ + ${SOUTDocker}/fastq/${FQ2} \ + ${qcPEFQ1} ${qcSEFQ1} \ + ${qcPEFQ2} ${qcSEFQ2} \ + ILLUMINACLIP:${adapter_fa}:2:30:10:5:true \ + LEADING:3 \ + TRAILING:3 \ + SLIDINGWINDOW:4:15 \ + AVGQUAL:2 \ + MINLEN:75 logger_ngseasy "[${NGSEASY_STEP}]:FastQC post Trimmomatic" ${LOGFILE}