fix(novaseq_bind_path): Reduce the bind path to simply it and remove …

…the ":"
Clinical-Genomics · Feb 6, 2021 · c24c173 · c24c173
1 parent 9742861
commit c24c173
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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