enable multithreading in trimmomatic calls and improve figure size fo…

…r association mapping results

src/assoc_mapping/case_control.R

@@ -78,7 +78,7 @@ odds_chrom$effect_str <- odds_chrom$Me/(odds_chrom$Mo+odds_chrom$Me)
 odds_chrom$effect_str[odds_chrom$effect_str>0.5] <- 0.5
 
 # Saving manhattan plot to pdf
-pdf(paste0(out_folder, "/../plots/","case_control_hits.pdf"), width=12, height=12)
+pdf(paste0(out_folder, "/../plots/","case_control_hits.pdf"), width=10, height=8)
 ggplot(data=odds_chrom, aes(x=BP/1000000, y=fisher)) + 
  geom_point(aes(col=effect_str), size = 2) + 
  facet_grid(~Chr, space='free_x', scales = 'free_x') + 

src/wgs_wild/bwa_wgs.sh

@@ -103,9 +103,9 @@ trimR=\$(echo \$reverse | sed 's%/\([^/]*\)$%/trim.\1%')
 trimFU=\$(echo \$trimF | sed 's/R1.fastq.gz$/R1U.fastq.gz/')
 trimRU=\$(echo \$trimR | sed 's/R2.fastq.gz$/R2U.fastq.gz/')
 
-# Trim low quality ends
+# Trim low quality ends 
 trimmomatic PE \$forward \$reverse \$trimF \$trimFU \$trimR \$trimRU \
- -trimlog ${logs}/${sample}-trim.log \
+ -trimlog ${logs}/${sample}-trim.log -threads $threads \
  LEADING:20 TRAILING:20
 
 # Mapping paired ends reads