nextflow.pbs: change position of NF option to facilitate bug tracking

src/nextflow.pbs

@@ -29,11 +29,11 @@ NEXTFLOW=/pbs/throng/lbmc/cl7/nextflow/${NF_VERSION}/nextflow
 NF=${SCRATCH}/${PROJECT}/src/${PIPELINE}.nf
 CONFIG=${SCRATCH}/${PROJECT}/src/${PIPELINE}.config
 DATA=${SCRATCH}/${PROJECT}/data
+NF_OPTIONS="-w \"${SCRATCH}/${PROJECT}/work/\" \
+-with-report \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html\" \
+-with-timeline \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html\" \
+-with-dag \"${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.pdf\""
 
-${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 \
+${NEXTFLOW} ${NF} -c ${CONFIG} -profile ccin2p3 ${NF_OPTIONS} \
 --fasta "${DATA}/fasta" \
 --results "${SCRATCH}/${PROJECT}/results/"
--w "${SCRATCH}/${PROJECT}/work/" \
--with-report "${SCRATCH}/${PROJECT}/results/${PIPELINE}_report.html" \
--with-timeline "${SCRATCH}/${PROJECT}/results/${PIPELINE}_timeline.html" \
--with-dag "${SCRATCH}/${PROJECT}/results/${PIPELINE}_dag.pdf"