From 92bcfdecee9a2de7be0675d316e21a082d600cbf Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Wed, 18 Sep 2024 16:38:47 +0200 Subject: [PATCH] add condition to run miniasm on long/hybrid mode only --- workflows/bacass.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/workflows/bacass.nf b/workflows/bacass.nf index e339689..4b2b0ed 100644 --- a/workflows/bacass.nf +++ b/workflows/bacass.nf @@ -240,7 +240,7 @@ workflow BACASS { // // MODULE: Miniasm, genome assembly, long reads // - if ( params.assembler == 'miniasm' ) { + if ( params.assembly_type != 'short' && params.assembler == 'miniasm' ) { MINIMAP2_ALIGN ( ch_for_assembly.map{ meta,sr,lr -> tuple(meta,lr) }, [[:],[]], @@ -280,6 +280,8 @@ workflow BACASS { ) ch_assembly = ch_assembly.mix( RACON.out.improved_assembly.dump(tag: 'miniasm') ) ch_versions = ch_versions.mix( RACON.out.versions ) + } else if (params.assembly_type == 'short' && params.assembler == 'miniasm') { + exit("Selected assembler ${params.assembler} cannot run on short reads") } //