Commit db8d35e4 authored by peguerin's avatar peguerin
Browse files

try checkpoint

parent f4b98142
......@@ -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}'''
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