Paths of general NGS tools.
Paths are preset and should not be changed unless you want to exchange a tool.
Paths of tools used in long-read pipeline.
Paths are preset and should not be changed unless you want to exchange a tool.
Paths of tools used in somatic pipeline.
Paths are preset and should not be changed unless you want to exchange a tool.
Paths of tools used in RNA pipeline.
Paths are preset and should not be changed unless you want to exchange a tool.
Paths of tools used for primer design.
Paths are preset and should not be changed unless you want to exchange a tool.
Paths of tools encapsulated in singularity containers.
Paths are preset and should not be changed unless you want to exchange a container.
This section contains path to important folders:
data_folder
- general data folder with downloaded database flat files.local_data
- local data folder. This folder is used to copy database files for annotation fromdata_folder
to a local temporary folder. The local temporary folder is usually on a SSD/NVME, so this will speed up the annotation.test_data_folder
- folder for test data. This folder is needed for unit tests and tool tests during pipeline development.project_folder
- folder that contains the NGS data. This folder has to be set for the NGSD integration (see below). Instead of providing a single path, it is also possible to provide project-type-specific paths - in this case the dictionary syntax of PHP is used, e.g.project_folder['diagnostic'] = /mnt/projects/diagnostic/
This section contains general settings:
copy_dbs_to_local_data
- Flag (true/false) that indicates if large database files (gnomAD, etc) are copied to the local folder.delete_fastq_files
- Flag (true/false) that indicates if FASTQ files are to be deleted after the BAM/CRAM file is created after mapping.cnv_bin_size_wgs
- Bin size used for CNV analysis of WGS samples.cnv_bin_size_shallow_wgs
- Bin size used for CNV analysis of shallow WGS samples.cnv_bin_size_longread_wgs
- Bin size used for CNV analysis of long-read WGS samples.use_bwa1
- Flag (true/false) that indicates if BWA mem should be used for mapping instead of BWA mem 2 (BWA mem 2 is faster, but needs more RAM).annotate_refseq_consequences
- Flag (true/false) that indicates if variant consequences based on RefSeq transcripts should be annotated in addition to variant consequences based on Ensembl transcripts.custom_columns
- Used to add custom annotations to the output VCF/GSvar file. Each entry consists of a colon-speparated list of VCF file, INFO field name in the source VCF (prefixed withCUSTOM_
in the annotated VCF) and column description. Provide the annotation using the dictionary syntax of PHP, e.g.custom_columns['NGSD_counts'] = "/mnt/data/dbs/NGSD/NGSD_germline.vcf.gz;COUNTS;NGSD counts"
.
This section contains settings to run the germline/somatic data analysis on a on-site Illumina Dragen server:
dragen_in
- Folder into which FASTQ data is copied for Dragen data analysis.dragen_out
- Folder into which Dragen output files are copied after the analysis.dragen_data
- Folder used as working directory on the Dragen server.dragen_genomes
- Folder containing genome files for Dragen on the Dragen server.dragen_log
- Folder used to write SGE logs of Dragen analyses.queues_dragen
- Comma-separated list of SGE queues for Dragen servers (one per server).use_dragen_sv_calling
- Flag (true/false) that indicates if SV calls produced by Dragen are used. If set tofalse
, SV calling based on Manta is used.
This section contains NGSD data (host, database name, credentials).
This section contains settings for automated data analysis via SGE:
queues_default
- Default SGE queues.queues_research
- Research SGE queues.queues_high_priority
- High-priority queues.queues_high_mem
- High-memory consumption queues (RNA).