fix results path

02_assembly/Snakefile

@@ -40,8 +40,8 @@ uniqRuns=dfrm.run.unique()
 rule all:
     input:
         expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
-        expand('../results/01_illuminapairedend/{run}.fastq', run=uniqRuns),
-        expand('../results/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
+        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}.log',run=uniqRuns)
 

02_assembly/rules/illuminapairedend.smk

@@ -8,7 +8,7 @@ rule illuminapairedend:
         R1=config["fichiers"]["folder_fastq"]+'{run}_R1.fastq.gz',
         R2=config["fichiers"]["folder_fastq"]+'{run}_R2.fastq.gz',
     output:
-        fq='../results/01_illuminapairedend/{run}.fastq'
+        fq='../results/02_assembly/01_illuminapairedend/{run}.fastq'
     conda:
         'envs/obitools_envs.yaml'
     singularity:

02_assembly/rules/remove_unaligned.smk

@@ -4,9 +4,9 @@ __license__ = "MIT"
 ### Remove unaligned sequence records
 rule remove_unaligned:
     input:
-        fq='../results/01_illuminapairedend/{run}.fastq'
+        fq='../results/02_assembly/01_illuminapairedend/{run}.fastq'
     output:
-        ali='../results/02_remove_unaligned/{run}.ali.fastq'
+        ali='../results/02_assembly/02_remove_unaligned/{run}.ali.fastq'
     conda:
         'envs/obitools_envs.yaml'
     singularity: