Commit 3648e68a authored by peguerin's avatar peguerin
Browse files

try checkpoint

parent b8e06699
......@@ -67,11 +67,11 @@ listChunks = [*range(1,(config['illuminapairedend']['nb_chunk']+1))]
rule all:
input:
expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
expand('../results/02_assembly/01_illuminapairedend/{run}_c{chunk}.fastq', run=uniqRuns, chunk=listChunks),
expand('../results/02_assembly/01_illuminapairedend/{run}_{chunk}.fastq', run=uniqRuns, chunk=listChunks),
expand('../results/02_assembly/01_illuminapairedend/{run}.fastq', run=uniqRuns),
expand('../results/02_assembly/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
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)
expand('../logs/02_assembly/01_illuminapairedend/{run}_{chunk}.log',run=uniqRuns, chunk=listChunks)
ruleorder: split_fastq > illuminapairedend > merge_chunks > remove_unaligned
......
......@@ -5,10 +5,10 @@ __license__ = "MIT"
## On scattered fastq chunk Paired end alignment then keep reads with quality > 40
checkpoint illuminapairedend:
input:
R1='../results/02_assembly/scaterred/{run}_R1_c{chunk}.fastq',
R2='../results/02_assembly/scaterred/{run}_R2_c{chunk}.fastq'
R1='../results/02_assembly/scaterred/{run}_R1_{chunk}.fastq',
R2='../results/02_assembly/scaterred/{run}_R2_{chunk}.fastq'
output:
fq='../results/02_assembly/01_illuminapairedend/{run}_c{chunk}.fastq'
fq='../results/02_assembly/01_illuminapairedend/{run}_{chunk}.fastq'
conda:
'../envs/obitools_envs.yaml'
singularity:
......
......@@ -8,13 +8,13 @@ rule split_fastq:
R1=config["fichiers"]["folder_fastq"]+'{run}_R1.fastq.gz',
R2=config["fichiers"]["folder_fastq"]+'{run}_R2.fastq.gz'
output:
R1='../results/02_assembly/scaterred/{run}_R1_c{chunk}.fastq',
R2='../results/02_assembly/scaterred/{run}_R2_c{chunk}.fastq'
R1='../results/02_assembly/scaterred/{run}_R1_{chunk}.fastq',
R2='../results/02_assembly/scaterred/{run}_R2_{chunk}.fastq'
conda:
'../envs/fastqsplitter_envs.yaml'
params:
R1=lambda wildcards: '-o '+' -o '.join([ '../results/02_assembly/scaterred/' + wildcards.run +'_R1_c'+ str(i) + '.fastq' for i in listChunks]),
R2=lambda wildcards: '-o '+' -o '.join([ '../results/02_assembly/scaterred/' + wildcards.run +'_R2_c'+ str(i) + '.fastq' for i in listChunks])
R1=lambda wildcards: '-o '+' -o '.join([ '../results/02_assembly/scaterred/' + wildcards.run +'_R1_'+ str(i) + '.fastq' for i in listChunks]),
R2=lambda wildcards: '-o '+' -o '.join([ '../results/02_assembly/scaterred/' + wildcards.run +'_R2_'+ str(i) + '.fastq' for i in listChunks])
shell:
'''CMD="fastqsplitter -i {input.R1}"; eval $CMD {params.R1}; CMD="fastqsplitter -i {input.R2}"; eval $CMD {params.R2};'''
......
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