Commit 9bc0b19f authored by peguerin's avatar peguerin
Browse files

fastq run forrmr config file

parent b67c7e4d

Snakefile

+9 −9
Original line number Diff line number Diff line
@@ -6,15 +6,15 @@ configfile: "config.yaml" 


rule all:

    input:

        expand("{folder}/{fastqf}_R1.fastq.gz", fastqf=config["fastqFiles"],folder=config["fastqFolderPath"]),        

        expand('assembled/{run}/{run}.fastq', run=RUNS),

        expand('assembled/{run}/{run}.ali.fastq', run=RUNS),

        expand('assembled/{run}/{run}.ali.assigned.fastq', run=RUNS),

        expand('assembled/{run}/{run}.unidentified.fastq', run=RUNS),

        expand('log/remove_unaligned/{run}.log',run=RUNS),

        expand('log/illuminapairedend/{run}.log',run=RUNS),

        expand('log/assign_sequences/{run}.log',run=RUNS),

        expand('log/split_sequences/{run}.log',run=RUNS)

        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"])





include: "rules/step1.smk"
 
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