Commit 21eadb6c authored by peguerin's avatar peguerin
Browse files

fix results path

parent ccb3e571
......@@ -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)
......
......@@ -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:
......
......@@ -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:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment