Commit 6b614624 authored by peguerin's avatar peguerin
Browse files

renaming step 02

parent 8d4870b7
......@@ -40,11 +40,12 @@ uniqRuns=dfrm.run.unique()
rule all:
input:
expand("{folder}{run}_R1.fastq.gz", run=uniqRuns,folder=config["fichiers"]["folder_fastq"]),
expand('01_illuminapairedend/{run}.fastq', run=uniqRuns),
expand('02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
expand('../99_log/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
expand('../99_log/02_assembly/01_illuminapairedend/{run}.log',run=uniqRuns)
expand('../results/01_illuminapairedend/{run}.fastq', run=uniqRuns),
expand('../results/02_remove_unaligned/{run}.ali.fastq', run=uniqRuns),
expand('../logs/02_assembly/02_remove_unaligned/{run}.log',run=uniqRuns),
expand('../logs/02_assembly/01_illuminapairedend/{run}.log',run=uniqRuns)
include: "../00_rules/assembly.smk"
include: "rules/illuminapairedend.smk"
include: "rules/remove_unaligned.smk"
__author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
### Paired end alignment then keep reads with quality > 40
rule illuminapairedend:
input:
R1=config["fichiers"]["folder_fastq"]+'{run}_R1.fastq.gz',
R2=config["fichiers"]["folder_fastq"]+'{run}_R2.fastq.gz',
output:
fq='01_illuminapairedend/{run}.fastq'
singularity:
config["singularity"]["obitools"]
log:
'../99_log/02_assembly/01_illuminapairedend/{run}.log'
params:
s_min=config["illuminapairedend"]["s_min"]
shell:
'''illuminapairedend -r {input.R2} {input.R1} --score-min={params.s_min} > {output.fq} 2> {log}'''
### Remove unaligned sequence records
rule remove_unaligned:
input:
fq='01_illuminapairedend/{run}.fastq'
output:
ali='02_remove_unaligned/{run}.ali.fastq'
singularity:
config["singularity"]["obitools"]
log:
'../99_log/02_assembly/02_remove_unaligned/{run}.log'
shell:
'''obigrep -p 'mode!=\"joined\"' {input.fq} > {output.ali} 2> {log}'''
__author__ = "Pierre-Edouard Guerin"
__license__ = "MIT"
### Remove unaligned sequence records
rule remove_unaligned:
input:
fq='01_illuminapairedend/{run}.fastq'
output:
ali='02_remove_unaligned/{run}.ali.fastq'
singularity:
config["singularity"]["obitools"]
log:
'../99_log/02_assembly/02_remove_unaligned/{run}.log'
shell:
'''obigrep -p 'mode!=\"joined\"' {input.fq} > {output.ali} 2> {log}'''
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