try checkpoint

02_assembly/Snakefile

@@ -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
 

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
 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:

02_assembly/rules/split_fastq.smk

@@ -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};'''