testing fix for wdl gtf_path syntax

broadinstitute · Jan 11, 2025 · 422ad3b · 422ad3b
1 parent 6f10319
commit 422ad3b
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/pipelines/skylab/atac/atac.wdl b/pipelines/skylab/atac/atac.wdl
@@ -521,6 +521,7 @@ task CreateFragmentFile {
     String atac_nhash_id = ""
     String input_id
     Int atac_expected_cells = 3000
+    String gtf_path = annotations_gtf
   }
 
   parameter_meta {
@@ -605,7 +606,7 @@ task CreateFragmentFile {
     # Add GTF to uns field
     
     # Original path from args.annotation_file
-    gtf_path = str(~{annotations_gtf})  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
+    gtf_path = "~{gtf_path}"  # e.g., '/cromwell_root/gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_v43.annotation.gtf'
 
     # # Transform the path
     # if annotation_gtf.startswith('/cromwell_root/'):

diff --git a/tasks/skylab/H5adUtils.wdl b/tasks/skylab/H5adUtils.wdl
@@ -79,7 +79,7 @@ task OptimusH5adGeneration {
           ~{"--input_name_metadata_field " + input_name_metadata_field} \
           --count_matrix ~{sparse_count_matrix} \
           --expression_data_type "exonic" \
-          --pipeline_version ~{pipeline_version}
+          --pipeline_version ~{pipeline_version} \
           --gtf_path $gtf_path
     else
         python3 /warptools/scripts/create_snrna_optimus_full_h5ad.py \