Merge pull request #20 from HumanCellAtlas/ds_fix_ss2_inputs_539

Update paths to reference files to match their new locations (539)

Author: samanehsan

adapter_pipelines/ss2_single_sample/adapter_example_static.json

@@ -1,13 +1,13 @@
 {
   "AdapterSmartSeq2SingleCell.gtf_file": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.primary_assembly.annotation.gtf",
   "AdapterSmartSeq2SingleCell.hisat2_ref_trans_name": "gencode_v27_trans_rsem",
-  "AdapterSmartSeq2SingleCell.rrna_intervals": "gs://hca-dcp-mint-test-data/reference/gencode.v27.rRNA.interval_list",
+  "AdapterSmartSeq2SingleCell.rrna_intervals": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode.v27.rRNA.interval_list",
   "AdapterSmartSeq2SingleCell.star_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_GencodeV27_Primary.tar",
   "AdapterSmartSeq2SingleCell.hisat2_ref_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/genome_snp_tran.tar.gz",
   "AdapterSmartSeq2SingleCell.genome_ref_fasta": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38.primary_assembly.genome.fa",
   "AdapterSmartSeq2SingleCell.hisat2_ref_trans_index": "gs://hca-dcp-mint-test-data/reference/HISAT2/gencode_v27_trans_rsem.tar.gz",
-  "AdapterSmartSeq2SingleCell.rsem_ref_index": "gs://hca-dcp-mint-test-data/reference/rsem_ref/gencode_v27_primary.tar",
-  "AdapterSmartSeq2SingleCell.gene_ref_flat": "gs://hca-dcp-mint-test-data/reference/GRCh38_gencode.v27.refFlat.txt",
+  "AdapterSmartSeq2SingleCell.rsem_ref_index": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/gencode_v27_primary.tar",
+  "AdapterSmartSeq2SingleCell.gene_ref_flat": "gs://hca-dcp-mint-test-data/reference/GRCh38_Gencode/GRCh38_gencode.v27.refFlat.txt",
   "AdapterSmartSeq2SingleCell.hisat2_ref_name": "genome_snp_tran",
   "AdapterSmartSeq2SingleCell.stranded":"NONE",
   "AdapterSmartSeq2SingleCell.reference_bundle": "bf51d668-3e14-4843-9bc7-5d676fdf0e01",