# ============================================================================
# Config file for RNA-seq
#
# ==================[ 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:
input_readtag: _R[12]_
input_pattern: '*fastq.gz'
# =========================================== Sections for the users

#############################################################################
# Genome section:
#
# :Parameters:
#
# - aligner: bowtie (no other mapper for now)
# - rRNA_file: path to an existing fasta file for ribosomal RNA (to be found in
#   genome_directory)
# - rRNA_feature: if rRNA_file is not provided, ribosomal RNA will be extract
#     from GFF using this feature name. It must be found. 
# - indexing: if indexing is set to True, the index for bowtie1 will be done as
#   well as the indexing of the aligner provided. If the files exists already, not
#   indexing is performed. If you want to force the index building despite the
#   presence of the index files, then, use the force_indexing parameter and set
#   it to True. Indexing is followed by force_indexing to make sure we do not
#   erase the index files, which may be large.
#
#   Only one annotation file must be provided. If so, we extract the feature
#   rRNA from the annotation, identifiy start/end and create fasta file on the
#   fly. You may simply provide an input fasta file with rRNA if you have one.
general:
    aligner: bowtie1
    rRNA_file: ''
    rRNA_feature: rRNA
    genbank_file: ''
    gff_file: 
    reference_file: 



#############################################################################
# bowtie1_mapping_rna used to align reads against ribosomal RNA
#
# :Parameters:
#
# - do: if unchecked, this rule is ignored
# - options: any options recognised by bowtie1 tool
# - threads: number of threads to be used
#
bowtie1_mapping_rna:
    do: true
    options: ''
    threads: 4




#############################################################################
#   MultiQC aggregates results from bioinformatics analyses across many
#   samples into a single report.
#
# :Parameters:
#
# - options: any options recognised by multiqc
# - output-directory: Create report in the specified output directory
# - config_file: by default, we use sequana RNA-seq multiqc_config file. 
#       If you want your own multiqc, fill this entry
multiqc:
    options: -f
    input_directory: .
    modules: ""
    config_file: multiqc_config.yaml