Merge pull request #86 from UPHL-BioNGS/erin-dev

Erin dev
UPHL-BioNGS · Dec 16, 2021 · 43fe3c3 · 43fe3c3
2 parents 56c007a + 2a121e3
commit 43fe3c3
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/Cecret.nf b/Cecret.nf
@@ -1538,7 +1538,7 @@ if (params.relatedness) {
       maxRetries 2
 
       input:
-      file(consensus) from consensus_msa.concat(fastas_msa).concat(multifastas_msa)
+      file(consensus) from consensus_msa.concat(fastas_msa).concat(multifastas_msa).collect()
       file(reference_genome) from reference_genome_msa
 
       output:
@@ -1555,9 +1555,9 @@ if (params.relatedness) {
         echo "mafft version:" >> $log_file
         mafft --version 2>&1 >> $log_file
 
-        for fasta in !{task.process}/!{consensus}
+        for fasta in !{consensus}
         do
-          cat $fasta >> ultimate.fasta
+          cat $fasta >> !{task.process}/ultimate.fasta
         done
 
         mafft --auto \
@@ -1578,7 +1578,7 @@ if (params.relatedness) {
       container 'nextstrain/nextalign:latest'
 
       input:
-      file(consensus) from consensus_msa.concat(fastas_msa).concat(multifastas_msa)
+      file(consensus) from consensus_msa.concat(fastas_msa).concat(multifastas_msa).collect()
       path(dataset) from prepped_nextalign
 
       output: