try checkpoint

02_assembly/rules/chunk_illuminapairedend.smk

@@ -3,7 +3,7 @@ __license__ = "MIT"
 
 
 ## On scattered fastq chunk Paired end alignment then keep reads with quality > 40
-rule illuminapairedend:
+checkpoint illuminapairedend:
     input:
         R1='../results/02_assembly/scaterred/{run}_R1_c{chunk}.fastq',
         R2='../results/02_assembly/scaterred/{run}_R2_c{chunk}.fastq'
@@ -21,3 +21,18 @@ rule illuminapairedend:
     shell:
         '''illuminapairedend -r {input.R2} {input.R1} --score-min={params.s_min} > {output.fq} 2> {log};'''
 
+
+def get_chunks(wildcards):
+    meschunks = checkpoints.illuminapairedend.get(**wildcards).output.fq
+    return meschunks
+
+
+rule merge_chunks:
+    input:
+        get_chunks
+    output:
+        fq='../results/02_assembly/01_illuminapairedend/{run}.fastq'
+    shell:
+        '''cat {input} > {output}'''
+
+