# ============================================================================
# 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.
#
# If input_directory set, use input_extension if provided (otherwise use *.fastq.gz)
# input_extension should be without * . EG ".fasta" or ".bam"
# ============================================================================


input_directory: 
input_extension:
input_readtag:
input_pattern: "*.fasta"
input_samples: 


#############################################################################
#
# - genomeSize: <number>[g|m|k]
# - threads: number of threads to be used
# - techno: one of the technology the reads were generated with
# - options: any valid options supported by CANU
#
#  :reference: http://canu.readthedocs.io/
#
# techno_choice__ = ["-pacbio-raw", "-pacbio-corrected", "-nanopore-raw", "-nanopore-corrected"]
# 
canu:
    genomeSize: 4.1m
    threads: 4
    techno_choice: -pacbio-raw
    options: ''

###################################################################
#
#
# - species_choice
# - mode_choice: Specify which BUSCO analysis mode to run
#
# mode_choice__ = ["genome", "transcriptome", "proteins"]
# species_choice__ = ['actinobacteria_odb9', 'actinopterygii_odb9', 'alveolata_stramenophiles_ensembl', 'arthropoda_odb9', 'ascomycota_odb9', 'aves_odb9', 'bacillales_odb9', 'bacteria_odb9', 'bacteroidetes_odb9', 'basidiomycota_odb9', 'betaproteobacteria_odb9', 'clostridia_odb9', 'cyanobacteria_odb9', 'deltaepsilonsub_odb9', 'dikarya_odb9', 'diptera_odb9', 'embryophyta_odb9', 'endopterygota_odb9', 'enterobacteriales_odb9', 'euarchontoglires_odb9', 'eukaryota_odb9', 'eurotiomycetes_odb9', 'firmicutes_odb9', 'fungi_odb9', 'gammaproteobacteria_odb9', 'hymenoptera_odb9', 'insecta_odb9', 'lactobacillales_odb9', 'laurasiatheria_odb9', 'mammalia_odb9', 'metazoa_odb9', 'microsporidia_odb9', 'nematoda_odb9', 'pezizomycotina_odb9', 'proteobacteria_odb9', 'protists_ensembl', 'rhizobiales_odb9', 'saccharomyceta_odb9', 'saccharomycetales_odb9', 'sordariomyceta_odb9', 'spirochaetes_odb9', 'tenericutes_odb9', 'tetrapoda_odb9', 'vertebrata_odb9']
busco:
    threads: 4
    mode_choice: genome
    options: ''
    species_choice: proteobacteria_odb9
