## initialize
ln -s '${bam}' alignment.bam &&
ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&

## Possibly new options bam_chunk and bam_workers. Should we be setting these?

## run
medaka inference
## optional
--debug ## increase log level
--threads \${GALAXY_SLOTS:-4}
--batch_size $batch_size
#if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
    --regions
    #if $regions_cond.regions_sel == 'custom'
        '$regions_cond.custom'
    #else if $regions_cond.regions_sel == 'bed'
        '$regions_cond.bed'
    #end if
#end if
--chunk_len $chunk_len
--chunk_ovlp $chunk_ovlp
--model $model
$check_output
$save_features
#if $RG
    --RG '$RG'
#end if
#if $tag_name
    --tag_name '$tag_name'
#end if
#if str($tag_value):
    --tag_value $tag_value
#end if
$tag_keep_missing
## required
alignment.bam ## bam
'$out_result'  2>&1 | tee log.txt