# ============================================================================
# Config file for Quality Control
# ==========================================[ Sections for the users ]========
#
# One of input_directory, input_pattern and input_samples must be provided
# If input_directory provided, use it otherwise if input_pattern provided,
# use it, otherwise use input_samples.
# ============================================================================
input_directory: /home/cokelaer/Data/Pacbio/pacbio_qc/data
input_readtag: ''
input_pattern: '*.bam'

# if you have some samples starting with prefix to bed removed,
# uncomment this line and fill the list ,
# extra_prefixes_to_strip: ["lima_output"]


apptainers:
    graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
    sequana: "https://zenodo.org/record/7341710/files/sequana_tools_0.14.5.img"



bam_to_fasta:
    thread: 4


######################################################
# Taxonomic analysis
#
# Provide as many databases as you want. They will be 
# used sequentially.
kraken:
    do: false
    thread: 4
    databases:
        - ~/.config/sequana/kraken2_dbs/viruses_masking/


##############################################################################
# MultiQC section
#
# :Parameters:
#
# - options: string with any valid MultiQC options

multiqc:
    input_directory: .
    options: -p -f
    modules: sequana_pacbio_qc
    config_file: ''