autoDL.conf.example

BASE_DIR=/basedir/of/all/your/sequence/data/
# if you have multiple sequencers outputing in several dirs -- then you need to adjust autoDL.sh variable RUN_PATHS accordingly and you migh hav to modifiy the assignVariables function (e.g. add an HiSeq section or so)
# you need in autoDLDir a sampleSheets.txt file which will describe your samplesheets names and associated BED files and potentially keywords lying in the descritpion field of the samplesheets which will also point to a particualr BED file (in case you can't name your samplesheets as you like).
MINISEQ_RUNS_DIR=${BASE_DIR}MiniSeq/
MISEQ_RUNS_DIR=${BASE_DIR}MiSeqDx/RUO/
NEXTSEQ_RUNS_DIR=${BASE_DIR}NAS_CHU/NEXTSEQ/runs/converted/
NEXTSEQ_RUNS_DEST_DIR=${BASE_DIR}NextSeq/
MINISEQ_MAX_DEPTH=3
MISEQ_MAX_DEPTH=2
NEXTSEQ_MAX_DEPTH=2
MINISEQ_TRIGGER_FILE=AnalysisLog.txt
MISEQ_TRIGGER_FILE=AnalysisLog.txt
NEXTSEQ_TRIGGER_FILE=bcl2fastq/bcl2fastq.log
MINISEQ_TRIGGER_EXPR="Total execution time"
MISEQ_TRIGGER_EXPR="Total execution time"
NEXTSEQ_TRIGGER_EXPR="Processing completed"
MINISEQ_SAMPLESHEET_PATH=Alignment_*/*/SampleSheetUsed.csv
MISEQ_SAMPLESHEET_PATH=SampleSheet.csv
NEXTSEQ_SAMPLESHEET_PATH=bcl2fastq/SampleSheet.csv
AUTODL_DIR=./autoDLDir/
RUNS_FILE=${AUTODL_DIR}runs.txt
ROI_FILE=${AUTODL_DIR}sampleSheets.txt
ROI_DIR=/path/to/your/BED/files/
#_inputs.json WDL file
# https://software.broadinstitute.org/wdl/documentation/inputs.php
MOBIDL_JSON_DIR=/path/to/your/mobidlJson/models/
# if achab
ACHAB_TODO_DIR=/path/to/autoachab/dir/
DISEASE_ACHAB_DIR=${CONF_DIR}disease_achab/
INPUT_DIR=${AUTODL_DIR}
TMP_OUTPUT_DIR=/path/to/tmp_output/
# cromwell wrapper https://github.com/mobidic/Crom-wellWrapped
CWW=cww.sh
CROMWELL=/softs/cromwell.jar
# Cromwell options and conf file see
# https://cromwell.readthedocs.io/en/develop/
CROMWELL_OPTIONS=/softs/conf/options_mediummonster.json
CROMWELL_CONF=/softs/conf/mediummonster.conf
SERVICE=autoDLML.sh
RSYNC=/usr/bin/rsync
DOS2UNIX=/usr/bin/dos2unix
AWK=/usr/bin/awk
MULTIQC=/usr/bin/multiqc
PYTHON=/usr/bin/python
# if MobiCNV https://github.com/mobidic/MobiCNV
MOBICNV=MobiCNV/MobiCNV.py
BEDTOOLS=/usr/local/bin/bedtools
# if ifNCV https://github.com/SimCab-CHU/ifCNV
IFCNV=/path/to/ifCNV
# if ifcnv in conda env
CONDA=/path/to/condabin/conda
IFCNV_ENV=ifcnv_conda_env_name