try checkpoint

02_assembly/Snakefile

@@ -73,7 +73,7 @@ rule all:
         expand('../logs/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
         expand('../logs/02_assembly/01_illuminapairedend/{run}_c{chunk}.log',run=uniqRuns, chunk=listChunks)
 
-#ruleorder: split_fastq > illuminapairedend > remove_unaligned
+ruleorder: split_fastq > illuminapairedend > merge_chunks > remove_unaligned
 
 #include: "rules/illuminapairedend.smk"
 #include: "rules/remove_unaligned.smk"