compbio/ngseasy-trimmomatic repository overview

DOCKER_RUN="docker run -P -w /home/pipeman -e HOME=/home/pipeman -e USER=pipeman --user pipeman"

	${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