diff --git a/scripts/novaseq/demux-novaseq.sh b/scripts/novaseq/demux-novaseq.sh index f1071f35..78970d1f 100755 --- a/scripts/novaseq/demux-novaseq.sh +++ b/scripts/novaseq/demux-novaseq.sh @@ -47,5 +47,5 @@ log "Demux directory: ${DEMUX_DIR}" ################ log "start demultiplexing ${RUN_DIR}" -log "singularity exec --bind /home/proj/production/flowcells/novaseq:/home/proj/production/flowcells/novaseq/runs,/home/proj/production/flowcells/novaseq/demux,/home/proj/production/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/production/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1" -singularity exec --bind /home/proj/production/flowcells/novaseq:/home/proj/production/flowcells/novaseq/runs,/home/proj/production/flowcells/novaseq/demux,/home/proj/production/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/production/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1 +log "singularity exec --bind /home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/production/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1" +singularity exec --bind /home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/production/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1 diff --git a/scripts/novaseq/stage/demux-novaseq.sh b/scripts/novaseq/stage/demux-novaseq.sh index 381a1e38..9bfa75c5 100644 --- a/scripts/novaseq/stage/demux-novaseq.sh +++ b/scripts/novaseq/stage/demux-novaseq.sh @@ -48,5 +48,5 @@ log "Demux directory: ${DEMUX_DIR}" ################ log "start demultiplexing ${RUN_DIR}" -log "singularity exec --bind /home/proj/stage/flowcells/novaseq:/home/proj/stage/flowcells/novaseq/runs,/home/proj/stage/flowcells/novaseq/demux,/home/proj/stage/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/stage/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1" -singularity exec --bind /home/proj/stage/flowcells/novaseq:/home/proj/stage/flowcells/novaseq/runs,/home/proj/stage/flowcells/novaseq/demux,/home/proj/stage/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/stage/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1 +log "singularity exec --bind /home/proj/stage/flowcells/novaseq,/home/proj/stage/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/stage/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1" +singularity exec --bind /home/proj/stage/flowcells/novaseq,/home/proj/stage/flowcells/novaseq/"$SLURM_JOB_ID":/run/user/$(id -u) /home/proj/stage/demux-on-hasta/novaseq/container/bcl2fastq_v2-20-0.sif bcl2fastq --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${RUN_DIR} --output-dir ${DEMUX_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1