Merge branch 'master' into 'known-snps'

# Conflicts:
#   Snakefile

Snakefile

@@ -522,7 +522,7 @@ rule fastqc_raw:
     output:
         aux="{sample}/pre_process/raw_fastqc/.done.txt"
     singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
-    shell: "fastqc --nogroup -o {params.odir} {input.r1} {input.r2} "
+    shell: "fastqc --threads 4 --nogroup -o {params.odir} {input.r1} {input.r2} "
            "&& echo 'done' > {output.aux}"
 
 

cluster/sge_cluster.yml

@@ -7,7 +7,7 @@ align:
   threads: 8
   vmem: 4G
 markdup:
-  vmem: 10G
+  vmem: 20G
 baserecal:
   threads: 8
   vmem: 6G
@@ -24,6 +24,12 @@ genotype_gather:
 covstats:
   vmem: 6G
 multiqc:
-  vmem: 20G
+  vmem: 30G
 split_vcf:
   vmem: 20G
+fastqc_raw:
+  threads: 4
+fastqc_merged:
+  threads: 4
+fastqc_postqc:
+  threads: 4

src/safe_fastqc.sh

@@ -23,7 +23,7 @@ output_r1=${3}
 output_r2=${4}
 odir=${5}
 
-fastqc --nogroup -o ${odir} ${input_r1} ${input_r2}
+fastqc --threads 4 --nogroup -o ${odir} ${input_r1} ${input_r2}
 
 if [[ -f ${output_r1} ]]; then
     unzip -l ${output_r1} || head -c 0 ${output_r1} > ${output_r1}