Remove branch name parameter from multiple WDLs

broadinstitute · Jul 10, 2023 · 6e62f49 · 6e62f49
1 parent 1e83927
commit 6e62f49
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Showing 3 changed files with 1 addition and 8 deletions.
diff --git a/scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl b/scripts/variantstore/wdl/GvsBulkIngestGenomes.wdl
@@ -36,7 +36,6 @@ workflow GvsBulkIngestGenomes {
         Int? load_data_preemptible_override
         Int? load_data_maxretries_override
         # End GvsImportGenomes
-        String branch_name = "ah_var_store"
     }
 
     parameter_meta {
@@ -106,7 +105,6 @@ workflow GvsBulkIngestGenomes {
             load_data_maxretries_override = load_data_maxretries_override,
             load_data_preemptible_override = load_data_preemptible_override,
             load_data_gatk_override = gatk_override,
-            branch_name = branch_name,
             drop_state = drop_state,
     }
 

diff --git a/scripts/variantstore/wdl/GvsImportGenomes.wdl b/scripts/variantstore/wdl/GvsImportGenomes.wdl
@@ -29,7 +29,6 @@ workflow GvsImportGenomes {
     Int? load_data_maxretries_override
     Boolean process_vcf_headers = false
     File? load_data_gatk_override
-    String branch_name
   }
 
   Int max_auto_batch_size = 20000
@@ -100,7 +99,6 @@ workflow GvsImportGenomes {
         load_data_preemptible = effective_load_data_preemptible,
         load_data_maxretries = effective_load_data_maxretries,
         process_vcf_headers = process_vcf_headers,
-        branch_name = branch_name,
     }
   }
  if (process_vcf_headers) {
@@ -172,7 +170,6 @@ task LoadData {
     Boolean process_vcf_headers
 
     File? gatk_override
-    String branch_name
     Int load_data_preemptible
     Int load_data_maxretries
   }
@@ -243,14 +240,13 @@ task LoadData {
     bq --apilog=false --project_id=~{project_id} rm -f=true ~{temp_table}
 
     ## now we want to create a sub list of these samples (without the ones that have already been loaded)
-    curl --location --remote-name https://raw.githubusercontent.com/broadinstitute/gatk/~{branch_name}/scripts/variantstore/wdl/extract/curate_bulk_import_tsv.py
 
     # *re-*curated because the curation script is run again in this task. The curation script was already run at least
     # once before in a separate task to filter out already-loaded samples before the call to `LoadTask`. Here the
     # `LoadTask` job might be retried due to preemption so we only want to load the samples which still need loading.
     RECURATED_OUTPUT="bulk_import_recurated.tsv"
 
-    python3 curate_bulk_import_tsv.py \
+    python3 /gatk/scripts/variantstore/wdl/extract/curate_bulk_import_tsv.py \
       --samples-to-load $SAMPLE_MAP \
       --bulk-import-input-tsv ~{bulk_import_fofn} \
       --bulk-import-output-tsv $RECURATED_OUTPUT

diff --git a/scripts/variantstore/wdl/GvsUnified.wdl b/scripts/variantstore/wdl/GvsUnified.wdl
@@ -80,7 +80,6 @@ workflow GvsUnified {
             dataset_name = dataset_name,
             project_id = project_id,
             gatk_override = gatk_override,
-            branch_name = branch_name,
             interval_list = interval_list,
             drop_state = drop_state,
             sample_id_column_name = sample_id_column_name,