diff --git a/main.nf b/main.nf index c73f49c..8cf7dd2 100755 --- a/main.nf +++ b/main.nf @@ -6,6 +6,7 @@ include { HAPLINK_HAPLOTYPES as HAPLINK_ML_HAPLOTYPES } from './modules/haplink/ include { HAPLINK_HAPLOTYPES as HAPLINK_RAW_HAPLOTYPES } from './modules/haplink/haplotypes' include { HAPLINK_SEQUENCES } from './modules/haplink/sequences' include { HAPLINK_VARIANTS } from './modules/haplink/variants' +include { PREDICTHAPLO } from './modules/predicthaplo' include { MINIMAP2 } from './modules/minimap2' include { NANOFILT } form './modules/nanofilt' include { SHORAH_AMPLICON } from './modules/shorah/amplicon' @@ -76,6 +77,11 @@ workflow { ch_reference ) + PREDICTHAPLO( + ch_alignments, + ch_reference + ) + VIQUAS( ch_alignments, ch_reference