add-adapter

defaults

@@ -2,6 +2,7 @@
   "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
   "genome_directory":"oss://pgx-reference-data/reference/tophat2/",
   "idx_prefix":"tophat2",
+  "adapter": "oss://pgx-reference-data/reference/illumina_adapter/TruSeq3-PE.fa",
   "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
   "trimmomatic_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8",
   "tophat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat2:2.0.14",

inputs

@@ -2,6 +2,7 @@
     "{{ project_name }}.read1": "{{ read1 }}",
     "{{ project_name }}.read2": "{{ read2 }}",
     "{{ project_name }}.gtf": "{{ gtf }}",
+    "{{ project_name }}.adapter": "{ adapter }"
     "{{ project_name }}.genome_directory": "{{ genome_directory }}",
     "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
     "{{ project_name }}.baseout": "{{ baseout }}",