Snakemake 1000RNASeq ASE: add quality trimming threshold in Trimgalore rules

Snakemake/1000RNASeq_chicken/ASE/config_ase.yaml.example

@@ -39,6 +39,8 @@ data_dir : data
 
 # Filter on variant type if not already done (True or False)
 SNP_filter : True
+# quality trimming threshold used in trimgalore to remove low quality bases.
+trimming_quality : 15
 # minimum calling depth
 depth : 10
 # minimum percentage (between 0 and 1) of sample with known genotype

Snakemake/1000RNASeq_chicken/ASE/rules/TrimGalore.smk

@@ -45,12 +45,13 @@ rule trim_se:
     output:
         out=temp("Results_ASE/TrimGalore/{prefix}_trim.fastq.gz")
     params:
-        min_trim=lambda wildcards : str(int([ int(table[table["forward_read"] == f]["read_length"].tolist()[0]) for f in table["forward_read"] if f.startswith(wildcards.prefix)][0] / 3 ))
+        min_trim=lambda wildcards : str(int([ int(table[table["forward_read"] == f]["read_length"].tolist()[0]) for f in table["forward_read"] if f.startswith(wildcards.prefix)][0] / 3 )),
+        qual=config["trimming_quality"]
     log:
         "Results_ASE/TrimGalore/{prefix}_trimSe.log"
     shell:
         """
-        trim_galore --no_report_file --length {params.min_trim} --quality 0 -o `dirname {output.out}` {input} 2> {log}
+        trim_galore --no_report_file --length {params.min_trim} --quality {params.qual} -o `dirname {output.out}` {input} 2> {log}
         mv `dirname {output.out}`/{wildcards.prefix}*trimmed.fq.gz {output.out}
         """
 
@@ -64,10 +65,11 @@ rule trim_pe:
     log:
         "Results_ASE/TrimGalore/{prefix}_trimPe.log"
     params:
-        min_trim=lambda wildcards : str(int([ int(table[table["forward_read"] == f]["read_length"].tolist()[0]) for f in table["forward_read"] if f.startswith(wildcards.prefix)][0] / 3 ))
+        min_trim=lambda wildcards : str(int([ int(table[table["forward_read"] == f]["read_length"].tolist()[0]) for f in table["forward_read"] if f.startswith(wildcards.prefix)][0] / 3 )),
+        qual=config["trimming_quality"]
     shell:
         """
-        trim_galore --paired --no_report_file --length {params.min_trim} --quality 0 -o `dirname {output.out1}` {input} 2> {log}
+        trim_galore --paired --no_report_file --length {params.min_trim} --quality {params.qual} -o `dirname {output.out1}` {input} 2> {log}
         mv `dirname {output.out1}`/{wildcards.prefix}*_val_1.fq.gz {output.out1}
         mv `dirname {output.out1}`/{wildcards.prefix}*_val_2.fq.gz {output.out2}
         """