Merge 5c152f3 into 9c14679

Clinical-Genomics · Mar 23, 2021 · 1c3d487 · 1c3d487
2 parents 9c14679 + 5c152f3
commit 1c3d487
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Showing 3 changed files with 9 additions and 28 deletions.
diff --git a/demux/cli/basemask.py b/demux/cli/basemask.py
@@ -28,7 +28,7 @@ def basemask():
 @click.option(
     "-a",
     "--application",
-    type=click.Choice(["miseq", "nipt", "nova", "wes", "wgs"]),
+    type=click.Choice(["miseq", "nipt", "wes", "wgs"]),
     help="sequencing type",
 )
 def create(rundir, lane, application):
@@ -59,7 +59,7 @@ def create_basemask(sheet):
         basemask_index1 = "I" + str(len(index1)) + index1_n
 
         # index2 basemask
-        if read2 == 0:
+        if indexread2 == 0:
             click.echo(f"Y151,{basemask_index1},Y151")
         else:
             index2_n = "n" * (indexread2 - len(index2))
@@ -69,24 +69,8 @@ def create_basemask(sheet):
                 basemask_index2 = index2_n
             click.echo(f"Y{read1},{basemask_index1},{basemask_index2},Y{read2}")
 
-    def create_novaseq_basemask():
-        """ create the bcl2fastq basemask for novaseq flowcells"""
-
-        run_parameters_file = "RunParameters.xml"
-        run_params_tree = parse_run_parameters(run_parameters_file)
-
-        indexread1 = int(run_params_tree.findtext("IndexRead1NumberOfCycles"))
-        indexread2 = int(run_params_tree.findtext("IndexRead2NumberOfCycles"))
-        read1 = int(run_params_tree.findtext("Read1NumberOfCycles"))
-        read2 = int(run_params_tree.findtext("Read2NumberOfCycles"))
-
-        novaseq_basemask = f"Y{read1},I{indexread1},I{indexread2},Y{read2}"
-
-        click.echo(f"{novaseq_basemask}")
-
     def get_application_sheet(application):
         """ parse the samplesheet in the runs directory, based on the type of application """
-        sheet = None
         samplesheet = Path(rundir).joinpath("SampleSheet.csv")
         sheet_map = {
             "nipt": NIPTSamplesheet,
@@ -100,9 +84,6 @@ def get_application_sheet(application):
 
     def create_application_basemask(application):
         """ determine the basemask """
-        if application == "nova":
-            create_novaseq_basemask()
-        else:
-            create_basemask(get_application_sheet(application))
+        create_basemask(get_application_sheet(application))
 
     create_application_basemask(application)
diff --git a/scripts/novaseq/demux-novaseq.bash b/scripts/novaseq/demux-novaseq.bash
@@ -44,13 +44,13 @@ log "Starting NovaSeq demultiplexing"
 # Send a mail that demultiplexing has started
 cat ${PROJECTLOG} | mail -s "Starting demultiplexing of novaseq flowcell ${FC} on $(hostname)" $EMAIL
 
-BASEMASK=$(demux basemask create --application nova ${IN_DIR})
-UNALIGNED_DIR=Unaligned-${BASEMASK//,}
+
+UNALIGNED_DIR='Unaligned'
 
 # DEMUX !
 JOB_TITLE=Demux_${RUN}
-log "sbatch --wait -A ${SLURM_ACCOUNT} -J ${JOB_TITLE} -o ${PROJECTLOG} ${SCRIPT_DIR}/demux-novaseq.sh ${IN_DIR} ${OUT_DIR} ${BASEMASK} ${UNALIGNED_DIR}"
-RES=$(sbatch --wait -A ${SLURM_ACCOUNT} -J ${JOB_TITLE} -o ${PROJECTLOG} ${SCRIPT_DIR}/demux-novaseq.sh ${IN_DIR} ${OUT_DIR} ${BASEMASK} ${UNALIGNED_DIR})
+log "sbatch --wait -A ${SLURM_ACCOUNT} -J ${JOB_TITLE} -o ${PROJECTLOG} ${SCRIPT_DIR}/demux-novaseq.sh ${IN_DIR} ${OUT_DIR} ${UNALIGNED_DIR}"
+RES=$(sbatch --wait -A ${SLURM_ACCOUNT} -J ${JOB_TITLE} -o ${PROJECTLOG} ${SCRIPT_DIR}/demux-novaseq.sh ${IN_DIR} ${OUT_DIR} ${UNALIGNED_DIR})
 
 log "bcl2fastq finished!"
 

diff --git a/scripts/novaseq/demux-novaseq.sh b/scripts/novaseq/demux-novaseq.sh
@@ -49,5 +49,5 @@ mkdir -p /home/proj/production/flowcells/novaseq/"$SLURM_JOB_ID"
 ################
 
 log "start demultiplexing ${RUN_DIR}"
-log "singularity exec --bind /home/proj/production/demultiplexed-runs,/home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$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 ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1"
-singularity exec --bind /home/proj/production/demultiplexed-runs,/home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$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 ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1
+log "singularity exec --bind /home/proj/production/demultiplexed-runs,/home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$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} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1"
+singularity exec --bind /home/proj/production/demultiplexed-runs,/home/proj/production/flowcells/novaseq,/home/proj/production/flowcells/novaseq/"$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} --sample-sheet ${RUN_DIR}/SampleSheet.csv --barcode-mismatches 1