remove runs dir from rsync

Author: bpblanken

v03_pipeline/lib/tasks/dataproc/rsync_to_seqr_app_dirs.py

@@ -25,7 +25,7 @@ def rsync_command(src_path: str, dst_path: str) -> list[str]:
     return [
         '/bin/bash',
         '-cx',
-        f'mkdir -p {dst_path} && gsutil -qm rsync -rd -x .*runs.* {src_path} {dst_path} && sync {dst_path}',
+        f'mkdir -p {dst_path} && gsutil -qm rsync -rd {src_path} {dst_path} && sync {dst_path}',
     ]
 
 

v03_pipeline/lib/tasks/dataproc/rsync_to_seqr_app_dirs_test.py

@@ -90,21 +90,21 @@ def test_rsync_to_seqr_app_dirs_sync(
                     [
                         '/bin/bash',
                         '-cx',
-                        'mkdir -p /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL && gsutil -qm rsync -rd -x .*runs.* gs://test-hail-search-dir/GRCh38/SNV_INDEL /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL && sync /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL',
+                        'mkdir -p /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL && gsutil -qm rsync -rd gs://test-hail-search-dir/GRCh38/SNV_INDEL /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL && sync /var/seqr/seqr-hail-search-data/GRCh38/SNV_INDEL',
                     ],
                 ),
                 call(
                     [
                         '/bin/bash',
                         '-cx',
-                        'mkdir -p /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht && gsutil -qm rsync -rd -x .*runs.* gs://test-reference-data-dir/GRCh38/SNV_INDEL/high_af_variants.ht /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht && sync /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht',
+                        'mkdir -p /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht && gsutil -qm rsync -rd -x gs://test-reference-data-dir/GRCh38/SNV_INDEL/high_af_variants.ht /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht && sync /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/high_af_variants.ht',
                     ],
                 ),
                 call(
                     [
                         '/bin/bash',
                         '-cx',
-                        'mkdir -p /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht && gsutil -qm rsync -rd -x .*runs.* gs://test-reference-data-dir/GRCh38/SNV_INDEL/clinvar_path_variants.ht /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht && sync /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht',
+                        'mkdir -p /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht && gsutil -qm rsync -rd gs://test-reference-data-dir/GRCh38/SNV_INDEL/clinvar_path_variants.ht /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht && sync /var/seqr/seqr-reference-data/GRCh38/SNV_INDEL/clinvar_path_variants.ht',
                     ],
                 ),
             ],