Merge branch 'refs/heads/master' into release_3

hubmapconsortium · Oct 7, 2024 · f86411f · f86411f
2 parents 35eb941 + e740ae7
commit f86411f
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Showing 12 changed files with 6 additions and 14 deletions.
diff --git a/src/ingest-pipeline/airflow/dags/celldive_deepcell.py b/src/ingest-pipeline/airflow/dags/celldive_deepcell.py
@@ -248,7 +248,6 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            "--relax-path-checks",
             cwl_workflows["ome_tiff_pyramid"],
             "--ometiff_directory",
             ".",

diff --git a/src/ingest-pipeline/airflow/dags/codex_cytokit.py b/src/ingest-pipeline/airflow/dags/codex_cytokit.py
@@ -394,7 +394,6 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            '--relax-path-checks',
             cwl_workflows['ome_tiff_pyramid'],
             '--ometiff_directory',
             '.',

diff --git a/src/ingest-pipeline/airflow/dags/cwl/portal-containers b/src/ingest-pipeline/airflow/dags/cwl/portal-containers
diff --git a/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq b/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq
diff --git a/src/ingest-pipeline/airflow/dags/mibi_deepcell.py b/src/ingest-pipeline/airflow/dags/mibi_deepcell.py
@@ -241,7 +241,6 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            '--relax-path-checks',
             cwl_workflows['ome_tiff_pyramid'],
             '--ometiff_directory',
             '.',

diff --git a/src/ingest-pipeline/airflow/dags/multiome.py b/src/ingest-pipeline/airflow/dags/multiome.py
@@ -123,7 +123,6 @@ def build_cwltool_cmd1(**kwargs):
 
             command = [
                 *get_cwltool_base_cmd(tmpdir),
-                "--relax-path-checks",
                 "--outdir",
                 tmpdir / "cwl_out",
                 "--parallel",

diff --git a/src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py b/src/ingest-pipeline/airflow/dags/pas_ftu_segmentation.py
@@ -144,7 +144,6 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            "--relax-path-checks",
             cwl_workflows["ome_tiff_pyramid"],
             "--ometiff_directory",
             ".",

diff --git a/src/ingest-pipeline/airflow/dags/phenocycler_deepcell.py b/src/ingest-pipeline/airflow/dags/phenocycler_deepcell.py
@@ -241,7 +241,6 @@ def build_cwltool_cwl_ome_tiff_pyramid(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            "--relax-path-checks",
             cwl_workflows["ome_tiff_pyramid"],
             "--ometiff_directory",
             ".",

diff --git a/src/ingest-pipeline/airflow/dags/salmon_rnaseq.py b/src/ingest-pipeline/airflow/dags/salmon_rnaseq.py
@@ -105,7 +105,6 @@ def build_cwltool_cmd1(**kwargs):
 
             command = [
                 *get_cwltool_base_cmd(tmpdir),
-                "--relax-path-checks",
                 "--outdir",
                 tmpdir / "cwl_out",
                 "--parallel",

diff --git a/src/ingest-pipeline/airflow/dags/utils.py b/src/ingest-pipeline/airflow/dags/utils.py
@@ -1235,6 +1235,7 @@ def get_cwltool_base_cmd(tmpdir: Path) -> List[str]:
         # are created as *subdirectories* of 'cwl-tmp' and 'cwl-out-tmp'.
         "--tmpdir-prefix={}/".format(tmpdir / "cwl-tmp"),
         "--tmp-outdir-prefix={}/".format(tmpdir / "cwl-out-tmp"),
+        "--relax-path-checks",
     ]
 
 

diff --git a/src/ingest-pipeline/airflow/dags/visium.py b/src/ingest-pipeline/airflow/dags/visium.py
@@ -105,7 +105,6 @@ def build_cwltool_cmd1(**kwargs):
 
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            "--relax-path-checks",
             "--outdir",
             tmpdir / "cwl_out",
             "--parallel",
@@ -122,10 +121,10 @@ def build_cwltool_cmd1(**kwargs):
         command.append(data_dir / "raw/fastq/")
 
         command.append("--img_dir")
-        command.append(data_dir / "lab_processed/images/")
+        command.append(data_dir)
 
         command.append("--metadata_dir")
-        command.append(data_dir / "raw/")
+        command.append(data_dir)
 
         return join_quote_command_str(command)
 
@@ -175,7 +174,6 @@ def build_cwltool_cmd4(**kwargs):
         # this is the call to the CWL
         command = [
             *get_cwltool_base_cmd(tmpdir),
-            "--relax-path-checks",
             cwl_workflows[3],
             "--ometiff_directory",
             data_dir / "lab_processed/images/",

diff --git a/src/ingest-pipeline/airflow/dags/workflow_map.yml b/src/ingest-pipeline/airflow/dags/workflow_map.yml
@@ -66,7 +66,7 @@ workflow_map:
     'assay_type': 'sciATACseq'
     'workflow': 'sc_atac_seq_sci'
   - 'collection_type': 'generic_metadatatsv'
-    'assay_type': 'bulk RNA'
+    'assay_type': 'bulk-RNA'
     'workflow': 'salmon_rnaseq_bulk'
   - 'collection_type': 'generic_metadatatsv'
     'assay_type': 'sciRNAseq'