同步至HPC-v20190527版

增加Unaligned片段成分分析

inputs

@@ -1,17 +1,29 @@
 {
-    "{{ project_name }}.sample_ID": "{{ sample_id }}",
+    "{{ project_name }}.sample_id": "{{ sample_id }}",
     "{{ project_name }}.raw_fastq": "{{ raw_fastq }}",
+    "{{ project_name }}.sequencing_length": "{{ sequencing_length }}",
     "{{ project_name }}.adapter_seq": "{{ adapter_seq }}",
     "{{ project_name }}.randomBase_in_adapter": "{{ randomBase_in_adapter }}",
-    "{{ project_name }}.docker_fastp": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
-    "{{ project_name }}.cluster_config": "OnDemand ecs.sn2.large img-ubuntu-vpc",
-    "{{ project_name }}.disk_size": "200",
     "{{ project_name }}.qualified_quality_phred": "20",
     "{{ project_name }}.unqualified_percent_limit": "20",
-    "{{ project_name }}.n_base_limit": "5",
+    "{{ project_name }}.n_base_limit": "2",
     "{{ project_name }}.length_required": "16",
-    "{{ project_name }}.dir_index_mature": "oss://pgx-reference-data/miRNAseq/miRNA_mature/",
-    "{{ project_name }}.prefix_index_mature": "mature",
-    "{{ project_name }}.sum_unmatch_quality_limit": "40",
-    "{{ project_name }}.docker_bowtie": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bowtie:1.2.2-20190326"
+    "{{ project_name }}.max_mismatch_allowed": "1",
+    "{{ project_name }}.dir_index_miRNA": "oss://pgx-reference-data/miRBase/Release22.1/mature/index_bowtie/",
+    "{{ project_name }}.prefix_index_miRNA": "mature.human.U2T.expand",
+    "{{ project_name }}.dir_index_preMiRNA": "oss://pgx-reference-data/miRBase/Release22.1/hairpin/index_bowtie/",
+    "{{ project_name }}.prefix_index_preMiRNA": "hairpin.human.U2T",
+    "{{ project_name }}.dir_index_piRNA": "oss://pgx-reference-data/piRBase/",
+    "{{ project_name }}.prefix_index_piRNA": "piRNA_piRBase2.0_hsa",
+    "{{ project_name }}.dir_index_tRNA": "oss://pgx-reference-data/tRNA_UCSC/index_bowtie/",
+    "{{ project_name }}.prefix_index_tRNA": "tRNA",
+    "{{ project_name }}.dir_index_RNA": "oss://pgx-reference-data/GRCh38.p12_NCBI/Transcriptome/index_bowtie/",
+    "{{ project_name }}.prefix_index_RNA": "RNA",
+    "{{ project_name }}.dir_index_hg38": "oss://pgx-reference-data/GRCh38.p12_NCBI/Genome/index_bowtie/",
+    "{{ project_name }}.prefix_index_hg38": "GRCh.p12_genomic",
+    "{{ project_name }}.docker_fastqc": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
+    "{{ project_name }}.docker_fastp": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
+    "{{ project_name }}.docker_bowtie": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bowtie:1.2.2-20190326",
+    "{{ project_name }}.cluster_config": "OnDemand ecs.sn2.large img-ubuntu-vpc",
+    "{{ project_name }}.disk_size": "200"
 }