fix input

README.md

@@ -100,9 +100,11 @@ Hard filtration is applied, for GATK do not yet have the RNAseq training/truth r
 - `QD < 2.0`Qual By Depth values
 
 ```bash
+# GATK3, if you are using gatk4, please pay attention to the new arguments
 java -jar GenomeAnalysisTK.jar -T VariantFiltration -R hg_19.fasta -V input.vcf -window 35 -cluster 3 -filterName FS -filter "FS > 30.0" -filterName QD -filter "QD < 2.0" -o output.vcf 
 ```
 **Reference**
+
 1. GATK best practice https://software.broadinstitute.org/gatk/documentation/article.php?id=3891
 2. Sentieon manual https://support.sentieon.com/manual/RNA_call/rna/
 3. STAR github https://github.com/alexdobin/STAR

inputs

@@ -4,7 +4,7 @@
   "{{ project_name }}.PIdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.20.2",
   "{{ project_name }}.platform": "ILLUMINA",
   "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.disk_size": "500",
   "{{ project_name }}.SAdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/star:2.7.0",
   "{{ project_name }}.fastq_1": "{{ read1 }}",
   "{{ project_name }}.machine": "{{ machine }}",
@@ -12,7 +12,7 @@
   "{{ project_name }}.library": "{{ library }}",
   "{{ project_name }}.fastq_2": "{{ read2 }}",
   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
-  "{{ project_name }}.cluster_config": "{{ cluster if cluster != '' else 'OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc' }}",
+  "{{ project_name }}.cluster_config": "OnDemand ecs.sn1ne.8xlarge img-ubuntu-vpc",
   "{{ project_name }}.SAref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38_2.7.0d/",
   "{{ project_name }}.SAMdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
   "{{ project_name }}.STref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/",