# ============================================================================
# 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.
# ============================================================================

sequana_wrappers: "v23.11.18"

input_directory: '.'
input_pattern: '*fastq.gz'


# See sequana_pipetools.readthedocs.io for details about these 2 options
# common prefixes are removed. addition prefixes may be removed here
#extra_prefixes_to_strip = []
# in special cases, sample names can be extracted with a pattern
#sample_pattern: '{sample}.fastq.gz'


apptainers:
    falco: "https://zenodo.org/record/7014954/files/falco_1.0.0.img"
    fastqc: "https://zenodo.org/record/7923780/files/fastqc_0.12.1.img"
    graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
    multiqc: https://zenodo.org/record/10155626/files/multiqc_1.17.0.img


##############################################################################
# general section
#
# Choose one of the standard method to perform QC of your fastq data
#
# method_choice__ = ["fastqc", "falco"]
#
general:
    method_choice: fastqc

##############################################################################
# FastQC section
#
# :Parameters:
#
# - options: string with any valid FastQC options
fastqc:
    options: ''
    threads: 4
    resources:
        mem: 8G

##############################################################################
# Falco section
#
# :Parameters:
#
# - options: string with any valid FastQC options
falco:
    options: ''
    threads: 4
    resources:
        mem: 8G

##############################################################################
#
#
# - options: any multiqc options accepted. Note that if you use --comments, 
#   it will be appended to the existing --comments added inside sequana. 
#   By default, -p (create pictures) and -f (for overwritting) are used. 
# - indir: The input multiqc (default is local).
multiqc:
    do: true
    options: -p -f
    input_directory: "."
    modules: fastqc    # falco is not set; the fastqc module works for falco
    config_file: 
    resources:
        mem: 8G

plotting_and_stats:
    resources:
        mem: 8G