Commit ad7ceb29 authored by peguerin's avatar peguerin
Browse files

format rules

parent 69f6d531

Snakefile

+10 −10
Original line number Diff line number Diff line
@@ -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"