Merge pull request #52 from kids-first/feature/mb-pbta-20231016

🔨 Added new file type
kids-first · Oct 19, 2023 · 1c9075a · 1c9075a
2 parents 660e352 + 8d46821
commit 1c9075a
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Showing 38 changed files with 3 additions and 3,655 deletions.
diff --git a/REFS/cell_line_supplemental.txt b/REFS/cell_line_supplemental.txt
diff --git a/STUDY_CONFIGS/pbta_all_case_meta_config.json b/STUDY_CONFIGS/pbta_all_case_meta_config.json
@@ -221,17 +221,17 @@
         "manifests": {
             "cbtn": {
                 "table": "bix_genomics_file.sd_bhjxbdqk-genomics_file_manifest",
-                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
+                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","consensus_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
                 "out_file": "cbtn_genomics_file_manifest.txt"
             },
             "x01": {
                 "table": "bix_genomics_file.sd_bhjxbdqk_x01-genomics_file_manifest",
-                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
+                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","consensus_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
                 "out_file": "x01_genomics_file_manifest.txt"
             },
             "cbtn_extra": {
                 "table": "bix_genomics_file.sd_bhjxbdqk_x01_extra-genomics_file_manifest",
-                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
+                "file_type": ["RSEM_gene","annofuse_filtered_fusions_tsv","annotated_public_outputs","consensus_public_outputs","ctrlfreec_pval","ctrlfreec_info","ctrlfreec_bam_seg"],
                 "out_file": "cbtn_extra_genomics_file_manifest.txt"
             },
             "pnoc": {

diff --git a/scripts/2021-Sep-7_ETL_DEPRECATED/1a_merge_cavatica_manifests.py b/scripts/2021-Sep-7_ETL_DEPRECATED/1a_merge_cavatica_manifests.py
diff --git a/scripts/2021-Sep-7_ETL_DEPRECATED/1b_query_file_manifest.py b/scripts/2021-Sep-7_ETL_DEPRECATED/1b_query_file_manifest.py
diff --git a/scripts/2021-Sep-7_ETL_DEPRECATED/2_query_ds_by_bs_id.py b/scripts/2021-Sep-7_ETL_DEPRECATED/2_query_ds_by_bs_id.py