Commit ad7ceb29 authored by peguerin's avatar peguerin

format rules

parent 69f6d531
......@@ -7,14 +7,14 @@ configfile: "config.yaml"
rule all:
input:
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"]),
expand('assembled/{run}/{run}.unidentified.fastq', run=config["fastqFiles"]),
expand('log/remove_unaligned/{run}.log',run=config["fastqFiles"]),
expand('log/illuminapairedend/{run}.log',run=config["fastqFiles"]),
expand('log/assign_sequences/{run}.log',run=config["fastqFiles"]),
expand('log/split_sequences/{run}.log',run=config["fastqFiles"])
expand('01-assembly/{run}/{run}.fastq', run=config["fastqFiles"]),
expand('01-assembly/{run}/{run}.ali.fastq', run=config["fastqFiles"]),
expand('01-assembly/{run}/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
expand('01-assembly/{run}/{run}.unidentified.fastq', run=config["fastqFiles"]),
expand('99-log/remove_unaligned/{run}.log',run=config["fastqFiles"]),
expand('99-log/illuminapairedend/{run}.log',run=config["fastqFiles"]),
expand('99-log/assign_sequences/{run}.log',run=config["fastqFiles"]),
expand('99-log/split_sequences/{run}.log',run=config["fastqFiles"])
include: "rules/step1.smk"
\ No newline at end of file
include: "00-rules/assembly.smk"
include: "00-rules/demultiplex.smk"
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