try checkpoint

02_assembly/rules/chunk_illuminapairedend.smk

@@ -5,10 +5,10 @@ __license__ = "MIT"
 ## On scattered fastq chunk Paired end alignment then keep reads with quality > 40
 rule illuminapairedend:
     input:
-        R1='../results/02_assembly/scaterred/{run}_R1_{chunk}.fastq',
-        R2='../results/02_assembly/scaterred/{run}_R2_{chunk}.fastq'
+        R1='../results/02_assembly/scaterred/{run}_R1_c{chunk}.fastq',
+        R2='../results/02_assembly/scaterred/{run}_R2_c{chunk}.fastq'
     output:
-        fq='../results/02_assembly/01_illuminapairedend/{run}_{chunk}.fastq'
+        fq='../results/02_assembly/01_illuminapairedend/{run}_c{chunk}.fastq'
     conda:
         '../envs/obitools_envs.yaml'
     singularity: