Merge branch 'master' into release_1.5. update submodules and misc/tools

hubmapconsortium · Apr 2, 2021 · a904a56 · a904a56
2 parents cb4e85e + 15d92fd
commit a904a56
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Showing 11 changed files with 506 additions and 61 deletions.
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/cwl/sprm b/src/ingest-pipeline/airflow/dags/cwl/sprm
diff --git a/src/ingest-pipeline/airflow/dags/salmon_rnaseq.py b/src/ingest-pipeline/airflow/dags/salmon_rnaseq.py
@@ -320,9 +320,15 @@ def get_salmon_dag_params(assay: str) -> SequencingDagParameters:
     SequencingDagParameters(
         dag_id="salmon_rnaseq_10x",
         pipeline_name="salmon-rnaseq",
-        assay="10x",
+        assay="10x_v3",
         dataset_type="salmon_rnaseq_10x",
     ),
+    SequencingDagParameters(
+        dag_id="salmon_rnaseq_10x_sn",
+        pipeline_name="salmon-rnaseq",
+        assay="10x_v3_sn",
+        dataset_type="salmon_rnaseq_10x_sn",
+    ),
     get_salmon_dag_params("sciseq"),
     get_salmon_dag_params("slideseq"),
     get_salmon_dag_params("snareseq"),

diff --git a/src/ingest-pipeline/airflow/dags/sc_atac_seq.py b/src/ingest-pipeline/airflow/dags/sc_atac_seq.py
@@ -79,6 +79,7 @@ def build_cwltool_cmd1(**kwargs):
 
             command = [
                 *get_cwltool_base_cmd(tmpdir),
+                cwl_workflows[0],
                 "--assay",
                 params.assay,
                 "--outdir",

diff --git a/src/ingest-pipeline/airflow/dags/workflow_map.yml b/src/ingest-pipeline/airflow/dags/workflow_map.yml
@@ -58,7 +58,7 @@ workflow_map:
     'workflow': 'sc_atac_seq_sn'
   - 'collection_type': 'generic_metadatatsv'
     'assay_type': 'snRNAseq'
-    'workflow': 'salmon_rnaseq_10x'
+    'workflow': 'salmon_rnaseq_10x_sn'
   - 'collection_type': 'bulkatacseq_collection'
     'assay_type': 'ATACseq-bulk'
     'workflow': 'bulk_atacseq'