NationalGenomicsInfrastructure/ngi_pipeline

# This file should be placed under $HOME/.ngiconfig/ngi_config.yaml
# or its path exported as the environment variable NGI_CONFIG


analysis:
    best_practice_analysis:
        whole_genome_reseq:
            analysis_engine: ngi_pipeline.engines.piper_ngi
        qc:
            analysis_engine: ngi_pipeline.engines.qc_ngi
    top_dir: nobackup/NGI/analysis_ready
    sthlm_root: a2014205
    upps_root: a2015179
    base_root: /proj


database:
    record_tracking_db_path: /proj/a2014205/ngi_resources/record_tracking_database_nestor.sql


environment:
    project_id: a2014205
    conda_env: ngi
    ngi_scripts_dir: /proj/a2014205/software/ngi_pipeline/scripts
    flowcell_inbox: 
            - /proj/a2014205/archive
            - /proj/a2015179/archive


#genotyping:
#    lower_bound_cutoff: 0.9

logging:
    log_file: /proj/a2014205/ngi_resources/ngi_pipeline.log


paths: # Hard code paths here if you are that kind of a person
    binaries:
        #bowtie2:
        #fastqc:
        #fastq_screen:
    references:


piper:
    # Also can be set as an environmental variable $PIPER_QSCRIPTS_DIR
    path_to_piper_qscripts: /proj/a2014205/software/piper/qscripts
    load_modules:
        - java/sun_jdk1.7.0_25
        - R/2.15.0
    threads: 16
    job_walltime:
        merge_process_variantcall: "10-00:00:00"
    shell_jobrunner: Shell
    #shell_jobrunner: ParallelShell --super_charge --ways_to_split 4
    #jobNative:
    #    - arg1
    #    - arg2
    #    - arg3

qc:
    load_modules:
        - bioinfo-tools
    fastqc:
        load_modules:
            - FastQC
        threads: 16
    fastq_screen:
        config_path: "/proj/a2014205/ngi_resources/fastq_screen.nestor.conf"
        load_modules:
            - bowtie2
            - fastq_screen
        subsample_reads: 200000
        threads: 1


slurm:
    extra_params:
        "--qos": "seqver"
    cores: 16


supported_genomes:
    "GRCh37": /proj/a2014205/piper_references/gatk_bundle/2.8/b37/human_g1k_v37.fasta

test_data:
    workflows:
        whole_genome_reseq:
            test_project:
                project_id: P0000
                project_name: "Y.Mom_15_01"
                bpa: "whole_genome_reseq"
            customize_config:
                analysis:
                    top_dir: /proj/a2014205/nobackup/NGI/test_data/
                charon:
                    charon_base_url: http://charon-dev.scilifelab.se
            local_files:
                flowcell: /proj/a2014205/nobackup/NGI/test_data/whole_genome_reseq/150424_ST-E00214_0031_BH2WY7CCXX
                #project: /proj/a2014205/nobackup/NGI/test_data/whole_genome_reseq/DATA/P0000
                vcf: /proj/a2014205/nobackup/NGI/test_data/whole_genome_reseq/vcf/
mail:
    # For testing you can change the default recipient here.
    # By default (when this value is not set) mails are sent to
    # "ngi_pipeline_operators@scilifelab.se" (see ngi_pipeline/utils/communication.py for details)
    # If you do not want to have mails, use the "quiet" option like
    #  scripts/print_running_jobs.py -q
    recipient: ngi_pipeline_operators@scilifelab.se