renaming step 02

02_assembly/Snakefile

@@ -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"
 

02_assembly/rules/illuminapairedend.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}'''

02_assembly/rules/remove_unaligned.smk

+__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}'''