bugfix

Snakefile

@@ -70,7 +70,7 @@ rule vcf_to_dosages:
         export prefix={wildcards.output_dir}/dosages
         mkdir -p $prefix
         echo "decompress and filter out: 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' ..."
-        bcftools filter -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' > $prefix/chr{wildcards.i}_.vcf
+        bcftools filter -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' {input.vcf_gz_file} > $prefix/chr{wildcards.i}_.vcf
         echo "add computing MAFs ..."
         bcftools $prefix/chr{wildcards.i}.vcf_ > $prefix/chr{wildcards.i}.vcf
         rm $prefix/chr{wildcards.i}_.vcf

scripts/slurm-snakemake.sh

 mkdir -p logs
-rm -f nohup.out
-touch nohup.out 
 nohup snakemake $1 \
     --jobs 99 \
     --use-singularity \