Merge fa5a651 into 51c93bb

4dn-dcic · Nov 9, 2020 · b25852e · b25852e
2 parents 51c93bb + fa5a651
commit b25852e
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Showing 4 changed files with 34 additions and 1 deletion.
diff --git a/chalicelib/checks/helpers/cgap_utils.py b/chalicelib/checks/helpers/cgap_utils.py
@@ -86,6 +86,11 @@
         "run_time": 12,
         "accepted_versions": ["v10", "v11", "v12", "v13", "v15", "v16", "v17"]
     },
+    # part II step 2b
+    "workflow_peddy": {
+        "run_time": 12,
+        "accepted_versions": ["v3"]
+    },
     # part III step 3
     'workflow_gatk-VQSR-check': {
         "run_time": 12,

diff --git a/chalicelib/checks/helpers/wfrset_cgap_utils.py b/chalicelib/checks/helpers/wfrset_cgap_utils.py
@@ -271,6 +271,16 @@
                 'description': 'processed output from cgap downstream pipeline'}
                 }
     },
+    {  # peddy_qc
+        'app_name': 'workflow_peddy',
+        'workflow_uuid': 'e17b9fe7-19e7-40d7-9c46-07bc7920ffc8',
+        'parameters': {},
+        "config": {
+            "instance_type": "t3.small",
+            "ebs_size": "1.2x",
+            "EBS_optimized": True
+        }
+    },
     {  # VEP
         'app_name': 'workflow_vep-parallel',
         'workflow_uuid': 'adc588cf-1c6c-4281-9193-9645726eb792',

diff --git a/chalicelib/checks/wfr_cgap_checks.py b/chalicelib/checks/wfr_cgap_checks.py
@@ -640,6 +640,7 @@ def cgapS2_status(connection, **kwargs):
     # list step names
     step1_name = 'workflow_gatk-CombineGVCFs'
     step2_name = 'workflow_gatk-GenotypeGVCFs-check'
+    step2b_name = 'workflow_peddy'
     step3_name = 'workflow_vep-parallel'
     step4_name = 'workflow_mutanno-micro-annot-check'
     step5_name = 'workflow_granite-qcVCF'
@@ -730,6 +731,7 @@ def cgapS2_status(connection, **kwargs):
 
         # if multiple sample, merge vcfs, if not skip it (CombineGVCF)
         if len(input_samples) > 1:
+            # Step1 Run CombineGVCFs
             s1_input_files = {'input_gvcfs': input_vcfs,
                               'chromosomes': '/files-reference/GAPFIGJVJDUY/',
                               'reference': '/files-reference/GAPFIXRDPDK5/'}
@@ -762,6 +764,22 @@ def cgapS2_status(connection, **kwargs):
                                                                   s2_input_files,  step2_name, 'vcf')
 
         if step2_status != 'complete':
+            step2b_status = ""
+        else:
+            # step 2b peddy qc
+            s2b_input_files = {"input_vcf": step2_output}
+            # str_qc_pedigree = str(json.dumps(qc_pedigree))
+            proband_first_sample_list = list(reversed(sample_ids))  # proband first sample ids
+            update_pars = {"parameters": {"family": "",
+                                          "pedigree": ""}
+                           }
+            s2b_tag = an_msa['@id'] + '_Part2step2b'
+            keep, step3c_status, step3c_output = cgap_utils.stepper(library, keep,
+                                                                    'step2b', s2b_tag, step2_output,
+                                                                    s2b_input_files,  step2b_name, '',
+                                                                    additional_input=update_pars, no_output=True)
+
+        if step2b_status != 'complete':
             step3_status = ""
         else:
             # run step3 VEP

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "foursight"
-version = "1.2.7"
+version = "1.2.8"
 description = "Serverless Chalice Application for Monitoring"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"