Commit 06e02c06 authored by peguerin's avatar peguerin
Browse files

path from config

parent e5443659

Snakefile

+1 −1
Original line number Diff line number Diff line
@@ -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"]),

rules/step1.smk

+2 −2
Original line number Diff line number Diff line
@@ -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: