#import re
#set $genomefiles = []
#for $genome in $genomes
    #set $input_name = $re.sub('[^\w\-_.]', '_',str($genome.element_identifier.split('/')[-1]))
ln -s '${genome}' '${input_name}.fasta' &&
$genomefiles.append($input_name)
#end for
    
dRep compare outdir

    -g
#for $genomefile in $genomefiles
    '${genomefile}.fasta'
#end for
    

#if $comp_clust.steps.select == 'default'
    
    --MASH_sketch '$comp_clust.steps.MASH_sketch'
    --P_ani $comp_clust.steps.P_ani
    $comp_clust.steps.multiround_primary_clustering
    --primary_chunksize $comp_clust.steps.primary_chunksize

    
    --S_algorithm '$comp_clust.steps.clustering.S_algorithm'
    #if $comp_clust.steps.clustering.S_algorithm == 'fastANI'
    $comp_clust.steps.clustering.greedy_secondary_clustering
    #else if $comp_clust.steps.clustering.S_algorithm == 'ANImf'
    
    --n_PRESET '$comp_clust.steps.clustering.n_PRESET'

    
    --coverage_method '$comp_clust.steps.clustering.coverage_method'

    #else if $comp_clust.steps.clustering.S_algorithm == 'ANIn'
    
    --n_PRESET '$comp_clust.steps.clustering.n_PRESET'

    
    --coverage_method '$comp_clust.steps.clustering.coverage_method'

    #end if
    --S_ani $comp_clust.steps.S_ani
    --cov_thresh $comp_clust.steps.cov_thresh

#else if $comp_clust.steps.select == 'SkipMash'
    --SkipMash
    
    --S_algorithm '$comp_clust.steps.clustering.S_algorithm'
    #if $comp_clust.steps.clustering.S_algorithm == 'fastANI'
    $comp_clust.steps.clustering.greedy_secondary_clustering
    #else if $comp_clust.steps.clustering.S_algorithm == 'ANImf'
    
    --n_PRESET '$comp_clust.steps.clustering.n_PRESET'

    
    --coverage_method '$comp_clust.steps.clustering.coverage_method'

    #else if $comp_clust.steps.clustering.S_algorithm == 'ANIn'
    
    --n_PRESET '$comp_clust.steps.clustering.n_PRESET'

    
    --coverage_method '$comp_clust.steps.clustering.coverage_method'

    #end if
    --S_ani $comp_clust.steps.S_ani
    --cov_thresh $comp_clust.steps.cov_thresh

#else
    
    --MASH_sketch '$comp_clust.steps.MASH_sketch'
    --P_ani $comp_clust.steps.P_ani
    $comp_clust.steps.multiround_primary_clustering
    --primary_chunksize $comp_clust.steps.primary_chunksize

    --SkipSecondary
#end if
    --clusterAlg '$comp_clust.clusterAlg'
    $comp_clust.run_tertiary_clustering


    --warn_dist $warning.warn_dist
    --warn_sim $warning.warn_sim
    --warn_aln $warning.warn_aln