Commit 06e02c06 authored by peguerin's avatar peguerin

path from config

parent e5443659
......@@ -6,7 +6,7 @@ configfile: "config.yaml"
rule all:
input:
expand("{folder}/{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand("{folder}{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand('assembled/{run}/{run}.fastq', run=config["fastqFiles"]),
expand('assembled/{run}/{run}.ali.fastq', run=config["fastqFiles"]),
expand('assembled/{run}/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
......
......@@ -5,8 +5,8 @@ __license__ = "MIT"
### Paired end alignment then keep reads with quality > 40
rule illuminapairedend:
input:
R1='raw/{run}_R1.fastq.gz',
R2='raw/{run}_R2.fastq.gz'
R1=config['fastqFolderPath']+'{run}_R1.fastq.gz',
R2=config['fastqFolderPath']+'{run}_R2.fastq.gz'
output:
fq='assembled/{run}/{run}.fastq'
singularity:
......
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