added conditionals

UPHL-BioNGS · Oct 17, 2023 · 8311517 · 8311517
1 parent aa3643c
commit 8311517
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/subworkflows/phylogenetic_analysis.nf b/subworkflows/phylogenetic_analysis.nf
@@ -16,13 +16,13 @@ workflow phylogenetic_analysis {
     ch_organism = Channel.empty()
 
     if (params.extras) {
-      ch_organism = ch_organism.mix(ch_top_hit.map { it -> tuple( it[0] , [ it[1].split("_")[0], it[1].split("_")[1]] )})
+      ch_organism = ch_organism.mix(ch_top_hit.map { it -> if (it) { tuple( it[0] , [ it[1].split("_")[0], it[1].split("_")[1]] )}})
 
       if ( params.fastani_include ) {
         ch_top_hit
           .map { it -> if (it) { tuple( it[1].split("_", 3)[2], it[2], it[1].split("_")[0, 1]) }}
           .groupTuple(by: 0)
-          .map { it -> tuple( it[1][0].baseName, it[1][0], it[2][0] ) }
+          .map { it -> if (it) { tuple( it[1][0].baseName, it[1][0], it[2][0] ) }}
           .unique()
           .set { ch_representative }