From 4111a993e5f26112c2cc9f19e8dc494c24fcc420 Mon Sep 17 00:00:00 2001 From: Matt Ruffalo Date: Mon, 22 Apr 2024 13:52:18 -0400 Subject: [PATCH 1/5] Use single ATAC-seq metadata file for 10X only, not SNARE-seq --- src/ingest-pipeline/airflow/dags/multiome.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/ingest-pipeline/airflow/dags/multiome.py b/src/ingest-pipeline/airflow/dags/multiome.py index b09b0d1d..5db7e7e5 100644 --- a/src/ingest-pipeline/airflow/dags/multiome.py +++ b/src/ingest-pipeline/airflow/dags/multiome.py @@ -43,6 +43,7 @@ "pipeline_name", "assay_rna", "assay_atac", + "requires_one_atac_metadata_file", ], ) @@ -123,9 +124,12 @@ def build_cwltool_cmd1(**kwargs): command.append(f"--fastq_dir_{component.lower()}") command.append(data_dir / Path(f"raw/fastq/{component}")) - for data_dir in data_dirs: + atac_metadata_files = [find_atac_metadata_file(data_dir) for data_dir in data_dirs] + if params.requires_one_atac_metadata_file: + if (count := len(atac_metadata_files)) != 1: + raise ValueError(f"Need 1 ATAC-seq metadata file, found {count}") command.append("--atac_metadata_file") - command.append(find_atac_metadata_file(data_dir)) + command.append(atac_metadata_files[0]) return join_quote_command_str(command) @@ -339,6 +343,7 @@ def get_simple_multiome_dag_params(assay: str) -> MultiomeSequencingDagParameter pipeline_name=f"multiome-{assay}", assay_rna=assay, assay_atac=assay, + requires_one_atac_metadata_file=False, ) @@ -348,6 +353,7 @@ def get_simple_multiome_dag_params(assay: str) -> MultiomeSequencingDagParameter pipeline_name="multiome-10x", assay_rna="10x_v3_sn", assay_atac="multiome_10x", + requires_one_atac_metadata_file=True, ), get_simple_multiome_dag_params("snareseq"), ] From 3c6012f0bcb9a6adc5e00a206e39bcc6ec4da27b Mon Sep 17 00:00:00 2001 From: Sean Donahue Date: Mon, 22 Apr 2024 14:17:40 -0400 Subject: [PATCH 2/5] Adding and using separate parameter for azimuth assay, using appropriate RNA assay value for 10x Multiome --- src/ingest-pipeline/airflow/dags/multiome.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/src/ingest-pipeline/airflow/dags/multiome.py b/src/ingest-pipeline/airflow/dags/multiome.py index 5db7e7e5..030ff026 100644 --- a/src/ingest-pipeline/airflow/dags/multiome.py +++ b/src/ingest-pipeline/airflow/dags/multiome.py @@ -43,6 +43,7 @@ "pipeline_name", "assay_rna", "assay_atac", + "assay_azimuth", "requires_one_atac_metadata_file", ], ) @@ -154,7 +155,7 @@ def build_cwltool_cmd2(**kwargs): "--secondary-analysis-matrix", "secondary_analysis.h5mu", "--assay", - params.assay_rna, + params.assay_azimuth, ] return join_quote_command_str(command) @@ -343,6 +344,7 @@ def get_simple_multiome_dag_params(assay: str) -> MultiomeSequencingDagParameter pipeline_name=f"multiome-{assay}", assay_rna=assay, assay_atac=assay, + assay_azimuth=assay, requires_one_atac_metadata_file=False, ) @@ -351,8 +353,9 @@ def get_simple_multiome_dag_params(assay: str) -> MultiomeSequencingDagParameter MultiomeSequencingDagParameters( dag_id="multiome_10x", pipeline_name="multiome-10x", - assay_rna="10x_v3_sn", + assay_rna="multiome_10x", assay_atac="multiome_10x", + assay_azimuth="10x_v3_sn", requires_one_atac_metadata_file=True, ), get_simple_multiome_dag_params("snareseq"), From 70d45d99083450d3ffc51593148bdba5512d6d8c Mon Sep 17 00:00:00 2001 From: Juan Puerto <=> Date: Mon, 6 May 2024 10:50:42 -0400 Subject: [PATCH 3/5] General: Bump portal-containers --- src/ingest-pipeline/airflow/dags/cwl/portal-containers | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ingest-pipeline/airflow/dags/cwl/portal-containers b/src/ingest-pipeline/airflow/dags/cwl/portal-containers index 00fd6df7..8270e467 160000 --- a/src/ingest-pipeline/airflow/dags/cwl/portal-containers +++ b/src/ingest-pipeline/airflow/dags/cwl/portal-containers @@ -1 +1 @@ -Subproject commit 00fd6df75a4311da4e50cc0173b6d6e50ddaf76d +Subproject commit 8270e467fe979d373df0cd448e7d38bd3bd85728 From 35dbaca3734a4246b5477c32a8d184c61f7fcac6 Mon Sep 17 00:00:00 2001 From: Juan Puerto <=> Date: Mon, 6 May 2024 15:36:34 -0400 Subject: [PATCH 4/5] General: Sync devel changes into this branch --- src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq b/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq index 8ca0aad5..6591870e 160000 --- a/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq +++ b/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq @@ -1 +1 @@ -Subproject commit 8ca0aad568a268586dd4b1697c237f88b72a98bf +Subproject commit 6591870e5784be2536a1a88d661dc3dbd7459367 From 9c56e3e2b23a97ceb747190dbf94c27815612fa2 Mon Sep 17 00:00:00 2001 From: Juan Puerto <=> Date: Mon, 6 May 2024 15:42:42 -0400 Subject: [PATCH 5/5] Revert "General: Sync devel changes into this branch" This reverts commit 35dbaca3734a4246b5477c32a8d184c61f7fcac6. --- src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq b/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq index 6591870e..8ca0aad5 160000 --- a/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq +++ b/src/ingest-pipeline/airflow/dags/cwl/salmon-rnaseq @@ -1 +1 @@ -Subproject commit 6591870e5784be2536a1a88d661dc3dbd7459367 +Subproject commit 8ca0aad568a268586dd4b1697c237f88b72a98bf