fixup(data-pipeline): fix paths in genes pipeline

broadinstitute · Nov 21, 2024 · b5dc36a · b5dc36a
1 parent babc94e
commit b5dc36a
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/data-pipeline/src/data_pipeline/pipelines/genes.py b/data-pipeline/src/data_pipeline/pipelines/genes.py
@@ -225,23 +225,23 @@
 # ---
 pipeline.add_download_task(
     "download_gtex_v10_tpm_data",
-    "gs://gnomad/resources/gtex/v10/GTEx_Analysis_2022-06-06_v10_RSEMv1.3.3_transcripts_tpm.txt.bgz",
-    f"/{external_sources_subdir}/gtex/v10/GTEx_Analysis_2022-06-06_v10_RSEMv1.3.3_transcripts_tpm.txt.bgz",
+    "https://storage.googleapis.com/adult-gtex/bulk-gex/v10/rna-seq/GTEx_Analysis_v10_RSEMv1.3.3_transcripts_tpm.txt.gz",
+    f"/{external_sources_subdir}/gtex/v10/GTEx_Analysis_v10_RSEMv1.3.3_transcripts_tpm.txt.gz",
 )
 
 pipeline.add_download_task(
     "download_gtex_v10_sample_attributes",
-    "gs://gnomad/resources/gtex/v10/GTEx_Analysis_v10_Open_Access_Reduced_Annotations_SampleAttributesDS.txt.bgz",
-    f"/{external_sources_subdir}/gtex/v10/GTEx_Analysis_v10_Open_Access_Reduced_Annotations_SampleAttributesDS.txt.bgz",
+    "https://storage.googleapis.com/adult-gtex/annotations/v10/metadata-files/GTEx_Analysis_v10_Annotations_SampleAttributesDS.txt",
+    f"/{external_sources_subdir}/gtex/v10/GTEx_Analysis_v10_Annotations_SampleAttributesDS.txt",
 )
 
 pipeline.add_task(
     "prepare_gtex_v10_expression_data",
     prepare_gtex_expression_data,
     "/gtex/gtex_v10_tissue_expression.ht",
     {
-        "transcript_tpms_path": "gs://gnomad-v4-data-pipeline/20240813_rhg_test/output/external_sources/gtex/v10/GTEx_Analysis_2022-06-06_v10_RSEMv1.3.3_transcripts_tpm.txt.bgz",
-        "sample_annotations_path": "gs://gnomad-v4-data-pipeline/20240813_rhg_test/output/external_sources/gtex/v10/GTEx_Analysis_v10_Open_Access_Reduced_Annotations_SampleAttributesDS.txt.bgz",
+        "transcript_tpms_path": "gs://gnomad-v4-data-pipeline/output/external_sources/gtex/v10/GTEx_Analysis_v10_RSEMv1.3.3_transcripts_tpm.txt.bgz",
+        "sample_annotations_path": pipeline.get_task("download_gtex_v10_sample_attributes"),
     },
     {
         "tmp_path": "/tmp",