Merge branch 'refs/heads/master' into release_3

hubmapconsortium · Feb 21, 2025 · ea19bf5 · ea19bf5
2 parents 462d88a + 0ec53aa
commit ea19bf5
Show file tree

Hide file tree

Showing 15 changed files with 80 additions and 49 deletions.
diff --git a/src/ingest-pipeline/airflow/dags/bulk_atacseq.py b/src/ingest-pipeline/airflow/dags/bulk_atacseq.py
@@ -108,6 +108,8 @@ def build_cwltool_cmd1(**kwargs):
         task_id="pipeline_exec",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd1')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/celldive_deepcell.py b/src/ingest-pipeline/airflow/dags/celldive_deepcell.py
@@ -165,7 +165,8 @@ def build_cwltool_cwl_segmentation(**kwargs):
         task_id="pipeline_exec_cwl_segmentation",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_segmentation')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -217,6 +218,7 @@ def build_cwltool_cmd_sprm(**kwargs):
         task_id="pipeline_exec_cwl_sprm",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -267,7 +269,7 @@ def build_cwltool_cmd_create_vis_symlink_archive(**kwargs):
         task_id="pipeline_exec_cwl_create_vis_symlink_archive",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_create_vis_symlink_archive')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -320,7 +322,7 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -370,7 +372,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_offsets",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_offsets')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -420,7 +422,7 @@ def build_cwltool_cmd_sprm_to_json(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_json",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_json')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -468,7 +470,7 @@ def build_cwltool_cmd_sprm_to_anndata(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_anndata",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_anndata')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/codex_cytokit.py b/src/ingest-pipeline/airflow/dags/codex_cytokit.py
@@ -191,8 +191,8 @@ def build_cwltool_cwl_illumination_first_stitching(**kwargs):
         task_id="pipeline_exec_cwl_illumination_first_stitching",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_illumination_first_stitching')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -238,6 +238,7 @@ def build_cwltool_cwl_cytokit(**kwargs):
         task_id="pipeline_exec_cwl_cytokit",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_cytokit')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -287,6 +288,7 @@ def build_cwltool_cwl_ometiff_second_stitching(**kwargs):
         task_id="pipeline_exec_cwl_ometiff_second_stitching",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ometiff_second_stitching')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -307,7 +309,7 @@ def build_cwltool_cwl_ometiff_second_stitching(**kwargs):
         task_id="delete_internal_pipeline_files",
         bash_command="""\
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         rm -rf cytokit new_tiles
         """,
     )
@@ -343,6 +345,7 @@ def build_cwltool_cmd_deepcelltypes(**kwargs):
         task_id="pipeline_exec_cwl_deepcelltypes",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_deepcelltypes')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -394,6 +397,7 @@ def build_cwltool_cmd_sprm(**kwargs):
         task_id="pipeline_exec_cwl_sprm",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -441,6 +445,7 @@ def build_cwltool_cmd_create_vis_symlink_archive(**kwargs):
         task_id="pipeline_exec_cwl_create_vis_symlink_archive",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_create_vis_symlink_archive')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -490,7 +495,7 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -538,6 +543,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_offsets",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_offsets')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -585,6 +591,7 @@ def build_cwltool_cmd_sprm_to_json(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_json",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_json')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -630,6 +637,7 @@ def build_cwltool_cmd_sprm_to_anndata(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_anndata",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_anndata')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/kaggle_2_segmentation.py b/src/ingest-pipeline/airflow/dags/kaggle_2_segmentation.py
@@ -143,8 +143,8 @@ def build_cwltool_cwl_segmentation(**kwargs):
         task_id="pipeline_exec_cwl_segmentation",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_segmentation')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -188,8 +188,7 @@ def build_cwltool_cwl_ome_tiff_pyramid_processed(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid_processed",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid_processed')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -235,8 +234,7 @@ def build_cwltool_cwl_ome_tiff_pyramid_raw(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid_raw",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid_raw')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -282,7 +280,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_offsets",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_offsets')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -328,7 +326,7 @@ def build_cwltool_cmd_ome_tiff_metadata(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_metadata",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_metadata')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/mibi_deepcell.py b/src/ingest-pipeline/airflow/dags/mibi_deepcell.py
@@ -163,8 +163,8 @@ def build_cwltool_cwl_segmentation(**kwargs):
         task_id="pipeline_exec_cwl_segmentation",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_segmentation')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -215,7 +215,7 @@ def build_cwltool_cmd_sprm(**kwargs):
         task_id="pipeline_exec_cwl_sprm",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -266,7 +266,7 @@ def build_cwltool_cmd_create_vis_symlink_archive(**kwargs):
         task_id="pipeline_exec_cwl_create_vis_symlink_archive",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_create_vis_symlink_archive')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -316,8 +316,7 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -367,7 +366,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_offsets",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_offsets')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -417,7 +416,7 @@ def build_cwltool_cmd_sprm_to_json(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_json",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_json')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -465,7 +464,7 @@ def build_cwltool_cmd_sprm_to_anndata(**kwargs):
         task_id="pipeline_exec_cwl_sprm_to_anndata",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_sprm_to_anndata')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/multiome.py b/src/ingest-pipeline/airflow/dags/multiome.py
@@ -250,6 +250,8 @@ def build_cwltool_cmd3(**kwargs):
             task_id="pipeline_exec",
             bash_command=""" \
             tmp_dir={{tmp_dir_path(run_id)}} ; \
+            mkdir -p "${tmp_dir}"/cwl_out ; \
+            cd "${tmp_dir}"/cwl_out ; \
             {{ti.xcom_pull(task_ids='build_cmd1')}} > $tmp_dir/session.log 2>&1 ; \
             echo $?
             """,
@@ -259,7 +261,7 @@ def build_cwltool_cmd3(**kwargs):
             task_id="pipeline_exec_azimuth_annotate",
             bash_command=""" \
             tmp_dir={{tmp_dir_path(run_id)}} ; \
-            cd "$tmp_dir"/cwl_out ; \
+            cd "${tmp_dir}"/cwl_out ; \
             {{ti.xcom_pull(task_ids='build_cmd2')}} >> $tmp_dir/session.log 2>&1 ; \
             echo $?
             """,
@@ -270,7 +272,7 @@ def build_cwltool_cmd3(**kwargs):
             bash_command=""" \
             tmp_dir={{tmp_dir_path(run_id)}} ; \
             ds_dir="{{ti.xcom_pull(task_ids="send_create_dataset")}}" ; \
-            cd "$tmp_dir"/cwl_out ; \
+            cd "${tmp_dir}"/cwl_out ; \
             mkdir -p hubmap_ui ; \
             cd hubmap_ui ; \
             {{ti.xcom_pull(task_ids='build_cmd3')}} >> $tmp_dir/session.log 2>&1 ; \

diff --git a/src/ingest-pipeline/airflow/dags/ometiff_pyramid.py b/src/ingest-pipeline/airflow/dags/ometiff_pyramid.py
@@ -126,7 +126,8 @@ def build_cwltool_cmd1(**kwargs):
         task_id="pipeline_exec_cwl1",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd1')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -159,7 +160,7 @@ def build_cwltool_cmd2(**kwargs):
         task_id="pipeline_exec_cwl2",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd2')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/ometiff_pyramid_ims.py b/src/ingest-pipeline/airflow/dags/ometiff_pyramid_ims.py
@@ -130,7 +130,8 @@ def build_cwltool_cmd1(**kwargs):
         task_id="pipeline_exec_cwl1",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd1')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -163,7 +164,7 @@ def build_cwltool_cmd2(**kwargs):
         task_id="pipeline_exec_cwl2",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd2')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,

diff --git a/src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py b/src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py
@@ -143,7 +143,8 @@ def build_cwltool_cwl_segmentation(**kwargs):
         task_id="pipeline_exec_cwl_segmentation",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        mkdir -p ${tmp_dir}/cwl_out ; \
+        mkdir -p "${tmp_dir}"/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_segmentation')}} > $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -187,7 +188,7 @@ def build_cwltool_cwl_ome_tiff_pyramid_processed(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid_processed",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
-        cd ${tmp_dir}/cwl_out ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid_processed')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -235,6 +236,7 @@ def build_cwltool_cwl_ome_tiff_pyramid_raw(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_pyramid_raw",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cwl_ome_tiff_pyramid_raw')}} >> $tmp_dir/session.log 2>&1 ; \
         echo $?
         """,
@@ -282,6 +284,7 @@ def build_cwltool_cmd_ome_tiff_offsets(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_offsets",
         bash_command=""" \
         tmp_dir={{tmp_dir_path(run_id)}} ; \
+        cd "${tmp_dir}"/cwl_out ; \
         {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_offsets')}} >> ${tmp_dir}/session.log 2>&1 ; \
         echo $?
         """,
@@ -331,7 +334,7 @@ def build_cwltool_cmd_ome_tiff_metadata(**kwargs):
         task_id="pipeline_exec_cwl_ome_tiff_metadata",
         bash_command=""" \
             tmp_dir={{tmp_dir_path(run_id)}} ; \
-            cd ${tmp_dir}/cwl_out ; \
+            cd "${tmp_dir}"/cwl_out ; \
             {{ti.xcom_pull(task_ids='build_cmd_ome_tiff_metadata')}} >> ${tmp_dir}/session.log 2>&1 ; \
             echo $?
             """,