Various adjustments to t1dgrs2 v2 pipeline

RTIInternational · Sep 25, 2024 · a929f55 · a929f55
1 parent 0a04366
commit a929f55
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Showing 6 changed files with 66 additions and 12 deletions.
diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json b/t1dgrs2_pipeline/v2.0/pipeline_config/entrypoint_calculate_t1dgrs2.json
@@ -11,6 +11,11 @@
             "default": "",
             "required": true
         },
+        "run_id": {
+            "type": "str",
+            "default": "",
+            "required": true
+        },
         "ref_bfile": {
             "type": "str",
             "default": "",
@@ -105,10 +110,11 @@
                     "inputs": {
                         "working_dir": "<inputs.working_dir>generate_file_for_export",
                         "output_dir": "<inputs.output_dir>generate_file_for_export",
+                        "run_id": "<inputs.run_id>",
                         "t1dgrs2_results_file": "<steps.calculate_t1dgrs2.outputs.results>",
                         "missingness_summary_file": "<steps.merge_missingness_summaries.outputs.merged_file>",
-                        "remove_file": "<inputs.control_samples>",
-                        "output_file": "<inputs.output_dir><inputs.sample_id>_for_export.csv",
+                        "remove_file": "<inputs.ref_samples>",
+                        "output_file": "<inputs.output_dir>generate_file_for_export/_for_export.csv",
                         "missing_hla_threshold": "<inputs.missing_hla_threshold>",
                         "missing_non_hla_threshold": "<inputs.missing_non_hla_threshold>"
 

diff --git a/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json b/t1dgrs2_pipeline/v2.0/pipeline_config/t1dgrs2_tasks.json
@@ -340,7 +340,7 @@
             }
         },
         "cmd": [
-            "/opt/extract_gvcf_variants.pl",
+            "/opt/merge_file_rows.sh",
             "--merge_list",
             "<inputs.merge_list>",
             "--merge-header_row_count",
@@ -412,6 +412,9 @@
             "output_dir": {
                 "type": "dir"
             },
+            "run_id": {
+                "type": "str"
+            },
             "t1dgrs2_results_file": {
                 "type": "file"
             },
@@ -421,9 +424,6 @@
             "remove_file": {
                 "type": "file"
             },
-            "output_file": {
-                "type": "str"
-            },
             "missing_hla_threshold": {
                 "type": "int",
                 "default": 1
@@ -442,7 +442,7 @@
             "--remove_file",
             "<inputs.remove_file>",
             "--output_file",
-            "<inputs.output_file>",
+            "<inputs.output_dir><inputs.run_id>_export.csv",
             "--missing_hla_threshold",
             "<inputs.missing_hla_threshold>",
             "--missing_non_hla_threshold",

diff --git a/t1dgrs2_pipeline/v2.0/scripts/batch_extract_gvcf_variants.py b/t1dgrs2_pipeline/v2.0/scripts/batch_extract_gvcf_variants.py
@@ -133,7 +133,7 @@ def get_running_workflows():
     if args.sequencing_provider == 'revvity':
         result = re.search(r'^\S+\-(\d+)_\d+-WGS.+\.hard-filtered.gvcf.gz$', file)
     elif args.sequencing_provider == 'genedx':
-        result = re.search(r'^(\d+).hard-filtered.gvcf.gz$', file)
+        result = re.search(r'^(\S+).hard-filtered.gvcf.gz$', file)
     if result:
         sample_id = result.group(1)
 

diff --git a/t1dgrs2_pipeline/v2.0/scripts/extract_gvcf_variants.pl b/t1dgrs2_pipeline/v2.0/scripts/extract_gvcf_variants.pl
@@ -24,8 +24,8 @@
     'sample_id=s' => \$sample_id,
     'gvcf=s' => \$gvcf,
     'variant_list=s' => \$variant_list,
-    'hla_variants_file' => \$hla_variants_file,
-    'non_hla_variants_file' => \$non_hla_variants_file,
+    'hla_variants_file=s' => \$hla_variants_file,
+    'non_hla_variants_file=s' => \$non_hla_variants_file,
     'out_prefix=s' => \$out_prefix,
     'pass_only:i' => \$pass_only,
     'filter_by_gq:i' => \$filter_by_gq,

diff --git a/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl b/t1dgrs2_pipeline/v2.0/scripts/generate_file_for_export.pl
@@ -40,11 +40,11 @@
 open(REMOVE, $remove_file);
 while(<REMOVE>) {
     chomp;
-    $remove{$_} = 1;
+    @F = split("\t");
+    $remove{$F[1]} = 1;
 }
 close REMOVE;
 
-
 # Open output file for writing
 open(OUTPUT_FILE, ">".$output_file);
 print OUTPUT_FILE join(",", "RTI_Accession","GRS2","Missingness_Filter")."\n";

diff --git a/wgs_qc_wf_tools/v1.0/README.md b/wgs_qc_wf_tools/v1.0/README.md
@@ -0,0 +1,48 @@
+<details>
+<summary>Usage</summary>
+
+``` shell
+# Launch step 1
+docker run -ti \
+    -v /rti-01/ngaddis:/rti-01/ngaddis \
+    -e task=launch_step_1 \
+    -e aws_access_key_id=<AWS_ACCESS_KEY_ID> \
+    -e aws_secret_access_key=<AWS_SECRET_ACCESS_KEY> \
+    -e parameters=<PARAMETERS> \
+    -e name=<NAME> \
+    -e role_arn=<ROLE_ARN> \  # Optional - default arn:aws:iam::515876044319:role/service-role/OmicsWorkflow-20240601210363
+    -e output_uri=<OUTPUT_URI> \  # Optional - default s3://rti-nida-iomics-oa-healthomics-output/
+    -e storage_capacity=<STORAGE_CAPACITY> \  # Optional - default 1000
+    -e workflow_id=<WORKFLOW_ID> \  # Optional - default 3565858
+    --rm rtibiocloud/wgs_qc_wf_tools:v1.0_1e4fbb0
+
+# Launch step 2
+docker run -ti \
+    -v /rti-01/ngaddis:/rti-01/ngaddis \
+    -e task=launch_step_2 \
+    -e aws_access_key_id=<AWS_ACCESS_KEY_ID> \
+    -e aws_secret_access_key=<AWS_SECRET_ACCESS_KEY> \
+    -e step_1_output_json=<STEP_1_OUTPUT_JSON> \
+    -e step_2_config_output_dir=<STEP_2_CONFIG_OUTPUT_DIR> \
+    -e role_arn=<ROLE_ARN> \  # Optional - default arn:aws:iam::515876044319:role/service-role/OmicsWorkflow-20240601210363
+    -e output_uri=<OUTPUT_URI> \  # Optional - default s3://rti-nida-iomics-oa-healthomics-output/
+    -e storage_capacity=<STORAGE_CAPACITY> \  # Optional - default 1000
+    -e minimum_ancestry_sample_count=<MINIMUM_ANCESTRY_SAMPLE_COUNT> \  # Optional - default 50
+    -e workflow_id=<WORKFLOW_ID> \  # Optional - default 5499609
+    --rm rtibiocloud/wgs_qc_wf_tools:v1.0_1e4fbb0
+```
+</details>
+
+
+<details>
+<summary>Build instructions</summary>
+
+``` shell
+cd biocloud_docker_tools/wgs_qc_wf_tools/v1.0
+
+# Local build
+docker build . -t wgs_qc_wf_tools/wgs_qc_wf_tools:v1.0
+
+```
+</details>
+