Commit 23e2123d authored by peguerin's avatar peguerin
Browse files

format like kallisto codes

parent 9b120c56
......@@ -8,11 +8,11 @@ rule illuminapairedend:
R1=config['fastqFolderPath']+'{run}_R1.fastq.gz',
R2=config['fastqFolderPath']+'{run}_R2.fastq.gz'
output:
fq='01-assembly/{run}/{run}.fastq'
fq='01-illuminapairedend/{run}.fastq'
singularity:
config["container"]
log:
'99-log/illuminapairedend/{run}.log'
'../99-log/01-assembly/01-illuminapairedend/{run}.log'
params:
s_min=config["illuminapairedend"]["s_min"]
shell:
......@@ -21,13 +21,13 @@ rule illuminapairedend:
### Remove unaligned sequence records
rule remove_unaligned:
input:
fq='01-assembly/{run}/{run}.fastq'
fq='01-illuminapairedend/{run}.fastq'
output:
ali='01-assembly/{run}/{run}.ali.fastq'
ali='02-remove_unaligned/{run}.ali.fastq'
singularity:
config["container"]
log:
'99-log/remove_unaligned/{run}.log'
'../99-log/01-assembly/02-remove_unaligned/{run}.log'
shell:
'''obigrep -p 'mode!=\"joined\"' {input.fq} > {output.ali} 2> {log}'''
__author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
configfile: "../config.yaml"
rule all:
input:
expand("{folder}{run}_R1.fastq.gz", run=config["fastqFiles"],folder=config["fastqFolderPath"]),
expand('01-illuminapairedend/{run}.fastq', run=config["fastqFiles"]),
expand('02-remove_unaligned/{run}.ali.fastq', run=config["fastqFiles"]),
expand('03-assign_sequences/{run}.ali.assigned.fastq', run=config["fastqFiles"]),
expand('03-assign_sequences/{run}.unidentified.fastq', run=config["fastqFiles"]),
expand('../99-log/01-assembly/02-remove_unaligned/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/01-illuminapairedend/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/03-assign_sequences/{run}.log',run=config["fastqFiles"]),
expand('../99-log/01-assembly/04-split_sequences/{run}.log',run=config["fastqFiles"])
include: "../00-rules/assembly.smk"
include: "../00-rules/demultiplex.smk"
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