save only the scaffolds fasta file

nf-modules-hub · Jul 18, 2020 · d7a7461 · d7a7461
1 parent 3cfad4e
commit d7a7461
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/main.nf b/main.nf
@@ -29,14 +29,14 @@ process spades {
     tuple genomeName, file(genomeReads) from ch_in_spades
 
     output:
-    path """${genomeName}""" into ch_out_spades
+    path """${genomeName}_scaffolds.fasta""" into ch_out_spades
 
 
     script:
 
     """
     spades.py -k 21,33,55,77 --careful --only-assembler --pe1-1 ${genomeReads[0]} --pe1-2 ${genomeReads[1]} -o ${genomeName} -t 2
+    cp ${genomeName}/scaffolds.fasta ${genomeName}_scaffolds.fasta 
     """
 }
 
-// TODO we only need to store the genomeName/scaffolds.fasta as genomeName_scaffolds.fasta