From 20a670f59e6ed1ed5774ddb3ea071943e6a77379 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Wed, 14 Jun 2023 13:20:14 -0400
Subject: [PATCH 1/5] [wfpm v0.8.0] started a new version sanity-check@0.1.2
 from sanity-check@0.1.1 which was released

---
 sanity-check/main.nf          | 2 +-
 sanity-check/pkg.json         | 2 +-
 sanity-check/tests/checker.nf | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/sanity-check/main.nf b/sanity-check/main.nf
index 3709e40..7d36390 100755
--- a/sanity-check/main.nf
+++ b/sanity-check/main.nf
@@ -24,7 +24,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.sanity-check'
diff --git a/sanity-check/pkg.json b/sanity-check/pkg.json
index a700cc4..76ec072 100644
--- a/sanity-check/pkg.json
+++ b/sanity-check/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "sanity-check",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "description": "Data submission sanity checks including verifying info from Clinical API",
     "main": "main.nf",
     "deprecated": false,
diff --git a/sanity-check/tests/checker.nf b/sanity-check/tests/checker.nf
index 96c1fce..c54bd4f 100755
--- a/sanity-check/tests/checker.nf
+++ b/sanity-check/tests/checker.nf
@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.1'
+version = '0.1.2'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.sanity-check'

From dbbaf6a7ef2065ae26772defbcf1c2b930516e74 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Wed, 14 Jun 2023 14:37:37 -0400
Subject: [PATCH 2/5] added check for existing normal sample

---
 sanity-check/main.py                          | 26 ++++++++++++++++---
 .../tests/input/bad_tumour_example.tsv        |  2 ++
 .../input/comparison_good_tumour_example.tsv  |  2 ++
 .../tests/input/good_tumour_example.tsv       |  2 ++
 .../tests/local_bad_tumour_example.json       |  6 +++++
 .../tests/local_good_tumour_example.json      |  6 +++++
 6 files changed, 41 insertions(+), 3 deletions(-)
 create mode 100644 sanity-check/tests/input/bad_tumour_example.tsv
 create mode 100644 sanity-check/tests/input/comparison_good_tumour_example.tsv
 create mode 100644 sanity-check/tests/input/good_tumour_example.tsv
 create mode 100644 sanity-check/tests/local_bad_tumour_example.json
 create mode 100644 sanity-check/tests/local_good_tumour_example.json

diff --git a/sanity-check/main.py b/sanity-check/main.py
index b5f3fbe..21e5a26 100755
--- a/sanity-check/main.py
+++ b/sanity-check/main.py
@@ -58,7 +58,7 @@ def main():
             args.clinical_url,
             args.api_token
         )
-        
+
         final_metadata=compile_metadata(
             metadata,
             clinical_metadata
@@ -67,6 +67,7 @@ def main():
                 final_metadata,
                 args.submission_song_url
         )
+
         if not args.force:
             check_analysis_exists(
                 final_metadata,
@@ -74,7 +75,7 @@ def main():
             )
         
         update_tsv(final_metadata,"updated_"+args.experiment_info_tsv)
-        
+    
 
 def load_tsv(experiment_info_tsv):
     metadata_dict = {}
@@ -145,12 +146,31 @@ def get_clinical(metadata,clinical_url,api_token):
 
         sample_ind=[ele for ele,sample in enumerate(response.json()['specimens'][specimen_ind[0]]['samples']) if sample['sampleId']==return_metadata['sample_id']]
         if len(sample_ind)!=1:
-            sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s'  was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id'],))
+            sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s'  was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id']))
         return_metadata['sample_type']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['sampleType']
         return_metadata['submitter_sample_id']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['submitterId']
+    if return_metadata['tumour_normal_designation']=="Tumour" and metadata.get("submitter_matched_normal_sample_id"):
+        check_tumour_sample_exists(metadata,response.json())
 
     return return_metadata
 
+def check_tumour_sample_exists(metadata,clinical_metadata):
+    submitter_id=metadata['submitter_matched_normal_sample_id']
+    
+    return_id=None
+    tumourNormalDesignation=None
+
+    for specimen in clinical_metadata['specimens']:
+        for samples in specimen['samples']:
+            if samples['submitterId']==submitter_id:
+                return_id=samples['submitterId']
+                tumourNormalDesignation=specimen["tumourNormalDesignation"]
+    if return_id==None:
+        sys.exit("'submitter_matched_normal_sample_id':%s was not found in study. Please verify '%s' has been registered." % (submitter_id,submitter_id))
+    if tumourNormalDesignation=="Tumour":
+        sys.exit("'submitter_matched_normal_sample_id':%s detected as tumour instead of normal. Please verify correct sample." % (submitter_id))
+
+
 def compile_metadata(metadata,clinical_metadata):
     
     ###Over-write metadata with clinical_metadata
diff --git a/sanity-check/tests/input/bad_tumour_example.tsv b/sanity-check/tests/input/bad_tumour_example.tsv
new file mode 100644
index 0000000..342165c
--- /dev/null
+++ b/sanity-check/tests/input/bad_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
\ No newline at end of file
diff --git a/sanity-check/tests/input/comparison_good_tumour_example.tsv b/sanity-check/tests/input/comparison_good_tumour_example.tsv
new file mode 100644
index 0000000..e4643fc
--- /dev/null
+++ b/sanity-check/tests/input/comparison_good_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/good_tumour_example.tsv b/sanity-check/tests/input/good_tumour_example.tsv
new file mode 100644
index 0000000..cc809e8
--- /dev/null
+++ b/sanity-check/tests/input/good_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
\ No newline at end of file
diff --git a/sanity-check/tests/local_bad_tumour_example.json b/sanity-check/tests/local_bad_tumour_example.json
new file mode 100644
index 0000000..61a3f24
--- /dev/null
+++ b/sanity-check/tests/local_bad_tumour_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/bad_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good_example.tsv"
+}
diff --git a/sanity-check/tests/local_good_tumour_example.json b/sanity-check/tests/local_good_tumour_example.json
new file mode 100644
index 0000000..f95725b
--- /dev/null
+++ b/sanity-check/tests/local_good_tumour_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/good_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good_tumour_example.tsv"
+}

From d6889c230f936e392b0f2115278f94abf14e7727 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 16 Jun 2023 10:20:06 -0400
Subject: [PATCH 3/5] add check to only allow `null` for `RNA-Seq` and
 `Targeted-Seq`

---
 sanity-check/main.py                                 | 12 ++++++++++--
 ...ad_tumour_example.tsv => bad1_tumour_example.tsv} |  0
 sanity-check/tests/input/bad2_tumour_example.tsv     |  2 ++
 .../tests/input/comparison_good1_tumour_example.tsv  |  2 ++
 .../tests/input/comparison_good2_tumour_example.tsv  |  2 ++
 ...d_tumour_example.tsv => good1_tumour_example.tsv} |  0
 sanity-check/tests/input/good2_tumour_example.tsv    |  2 ++
 ...ple.json => local_bad_tumour_badRef_example.json} |  2 +-
 ...le.json => local_bad_tumour_nullWGS_example.json} |  4 ++--
 sanity-check/tests/local_good_tumour_ts_example.json |  6 ++++++
 .../tests/local_good_tumour_wgs_example.json         |  6 ++++++
 11 files changed, 33 insertions(+), 5 deletions(-)
 rename sanity-check/tests/input/{bad_tumour_example.tsv => bad1_tumour_example.tsv} (100%)
 create mode 100644 sanity-check/tests/input/bad2_tumour_example.tsv
 create mode 100644 sanity-check/tests/input/comparison_good1_tumour_example.tsv
 create mode 100644 sanity-check/tests/input/comparison_good2_tumour_example.tsv
 rename sanity-check/tests/input/{good_tumour_example.tsv => good1_tumour_example.tsv} (100%)
 create mode 100644 sanity-check/tests/input/good2_tumour_example.tsv
 rename sanity-check/tests/{local_bad_tumour_example.json => local_bad_tumour_badRef_example.json} (77%)
 rename sanity-check/tests/{local_good_tumour_example.json => local_bad_tumour_nullWGS_example.json} (54%)
 create mode 100644 sanity-check/tests/local_good_tumour_ts_example.json
 create mode 100644 sanity-check/tests/local_good_tumour_wgs_example.json

diff --git a/sanity-check/main.py b/sanity-check/main.py
index 21e5a26..eea6113 100755
--- a/sanity-check/main.py
+++ b/sanity-check/main.py
@@ -149,11 +149,19 @@ def get_clinical(metadata,clinical_url,api_token):
             sys.exit("ID Mismatch detected. Sample_id:'%s'/'%s'  was not found within Specimen:'%s'/'%s' 's samples" % (metadata['submitter_sample_id'],return_metadata['sample_id'],metadata['submitter_specimen_id'],return_metadata['specimen_id']))
         return_metadata['sample_type']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['sampleType']
         return_metadata['submitter_sample_id']=response.json()['specimens'][specimen_ind[0]]['samples'][sample_ind[0]]['submitterId']
-    if return_metadata['tumour_normal_designation']=="Tumour" and metadata.get("submitter_matched_normal_sample_id"):
-        check_tumour_sample_exists(metadata,response.json())
+
+    if return_metadata['tumour_normal_designation']=="Tumour":
+        #WGS, WXS, RNA-Seq, Bisulfite-Seq, ChIP-Seq, Targeted-Seq
+        if metadata.get("submitter_matched_normal_sample_id"):
+            check_tumour_sample_exists(metadata,response.json())
+        else:
+            if metadata.get("experimental_strategy")!="RNA-Seq" and metadata.get("experimental_strategy")!= "Targeted-Seq":
+                sys.exit("Null entry for `submitter_matched_normal_sample_id` detected. For tumour `experiment_strategy` type %s ,this field is required and must reference a registered normal sample." % (metadata.get("experimental_strategy")))
 
     return return_metadata
 
+
+
 def check_tumour_sample_exists(metadata,clinical_metadata):
     submitter_id=metadata['submitter_matched_normal_sample_id']
     
diff --git a/sanity-check/tests/input/bad_tumour_example.tsv b/sanity-check/tests/input/bad1_tumour_example.tsv
similarity index 100%
rename from sanity-check/tests/input/bad_tumour_example.tsv
rename to sanity-check/tests/input/bad1_tumour_example.tsv
diff --git a/sanity-check/tests/input/bad2_tumour_example.tsv b/sanity-check/tests/input/bad2_tumour_example.tsv
new file mode 100644
index 0000000..834f45a
--- /dev/null
+++ b/sanity-check/tests/input/bad2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4
diff --git a/sanity-check/tests/input/comparison_good1_tumour_example.tsv b/sanity-check/tests/input/comparison_good1_tumour_example.tsv
new file mode 100644
index 0000000..e4643fc
--- /dev/null
+++ b/sanity-check/tests/input/comparison_good1_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuN1	QCMG	ILLUMINA	Illumina HiSeq 2000	WGS		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/comparison_good2_tumour_example.tsv b/sanity-check/tests/input/comparison_good2_tumour_example.tsv
new file mode 100644
index 0000000..5cf6f36
--- /dev/null
+++ b/sanity-check/tests/input/comparison_good2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count	gender	specimen_tissue_source	tumour_normal_designation	specimen_type	sample_type
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	Targeted-Seq		4	Female	Urine	Tumour	Metastatic tumour - metastasis to distant location	Total RNA
diff --git a/sanity-check/tests/input/good_tumour_example.tsv b/sanity-check/tests/input/good1_tumour_example.tsv
similarity index 100%
rename from sanity-check/tests/input/good_tumour_example.tsv
rename to sanity-check/tests/input/good1_tumour_example.tsv
diff --git a/sanity-check/tests/input/good2_tumour_example.tsv b/sanity-check/tests/input/good2_tumour_example.tsv
new file mode 100644
index 0000000..6e23ed7
--- /dev/null
+++ b/sanity-check/tests/input/good2_tumour_example.tsv
@@ -0,0 +1,2 @@
+type	program_id	submitter_sequencing_experiment_id	submitter_donor_id	submitter_specimen_id	submitter_sample_id	submitter_matched_normal_sample_id	sequencing_center	platform	platform_model	experimental_strategy	sequencing_date	read_group_count
+sequencing_experiment	TEST-CA	EXP-9	TEST_SUBMITTER_DONOR_ID_fpkyjwkleu	TEST_SUBMITTER_SPECIMEN_ID_fpkyjwkleuT1	TEST_SUBMITTER_SAMPLE_ID_fpkyjwkleuT1		QCMG	ILLUMINA	Illumina HiSeq 2000	Targeted-Seq		4
diff --git a/sanity-check/tests/local_bad_tumour_example.json b/sanity-check/tests/local_bad_tumour_badRef_example.json
similarity index 77%
rename from sanity-check/tests/local_bad_tumour_example.json
rename to sanity-check/tests/local_bad_tumour_badRef_example.json
index 61a3f24..e3fd86a 100644
--- a/sanity-check/tests/local_bad_tumour_example.json
+++ b/sanity-check/tests/local_bad_tumour_badRef_example.json
@@ -1,5 +1,5 @@
 {
-    "experiment_info_tsv": "input/bad_tumour_example.tsv",
+    "experiment_info_tsv": "input/bad1_tumour_example.tsv",
     "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
     "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
     "expected_output": "input/comparison_good_example.tsv"
diff --git a/sanity-check/tests/local_good_tumour_example.json b/sanity-check/tests/local_bad_tumour_nullWGS_example.json
similarity index 54%
rename from sanity-check/tests/local_good_tumour_example.json
rename to sanity-check/tests/local_bad_tumour_nullWGS_example.json
index f95725b..e3ebd08 100644
--- a/sanity-check/tests/local_good_tumour_example.json
+++ b/sanity-check/tests/local_bad_tumour_nullWGS_example.json
@@ -1,6 +1,6 @@
 {
-    "experiment_info_tsv": "input/good_tumour_example.tsv",
+    "experiment_info_tsv": "input/bad2_tumour_example.tsv",
     "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
     "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
-    "expected_output": "input/comparison_good_tumour_example.tsv"
+    "expected_output": "input/comparison_good_example.tsv"
 }
diff --git a/sanity-check/tests/local_good_tumour_ts_example.json b/sanity-check/tests/local_good_tumour_ts_example.json
new file mode 100644
index 0000000..5ccb5e7
--- /dev/null
+++ b/sanity-check/tests/local_good_tumour_ts_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/good2_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good2_tumour_example.tsv"
+}
diff --git a/sanity-check/tests/local_good_tumour_wgs_example.json b/sanity-check/tests/local_good_tumour_wgs_example.json
new file mode 100644
index 0000000..928f8b5
--- /dev/null
+++ b/sanity-check/tests/local_good_tumour_wgs_example.json
@@ -0,0 +1,6 @@
+{
+    "experiment_info_tsv": "input/good1_tumour_example.tsv",
+    "song_url": "https://submission-song.rdpc-qa.cancercollaboratory.org",
+    "clinical_url": "https://clinical.qa.argo.cancercollaboratory.org",
+    "expected_output": "input/comparison_good1_tumour_example.tsv"
+}

From e9f83f3ef8c167a9c4a688070eff6581b89f8a51 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 23 Jun 2023 16:36:36 -0400
Subject: [PATCH 4/5] rename function to `check_normal_sample_exists`

---
 sanity-check/main.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/sanity-check/main.py b/sanity-check/main.py
index eea6113..881cf0c 100755
--- a/sanity-check/main.py
+++ b/sanity-check/main.py
@@ -152,17 +152,17 @@ def get_clinical(metadata,clinical_url,api_token):
 
     if return_metadata['tumour_normal_designation']=="Tumour":
         #WGS, WXS, RNA-Seq, Bisulfite-Seq, ChIP-Seq, Targeted-Seq
-        if metadata.get("submitter_matched_normal_sample_id"):
-            check_tumour_sample_exists(metadata,response.json())
-        else:
-            if metadata.get("experimental_strategy")!="RNA-Seq" and metadata.get("experimental_strategy")!= "Targeted-Seq":
+        if metadata.get("experimental_strategy") in ['WGS', 'WXS']:
+            if metadata.get("submitter_matched_normal_sample_id"):
+                check_normal_sample_exists(metadata,response.json())
+            else:
                 sys.exit("Null entry for `submitter_matched_normal_sample_id` detected. For tumour `experiment_strategy` type %s ,this field is required and must reference a registered normal sample." % (metadata.get("experimental_strategy")))
 
     return return_metadata
 
 
 
-def check_tumour_sample_exists(metadata,clinical_metadata):
+def check_normal_sample_exists(metadata,clinical_metadata):
     submitter_id=metadata['submitter_matched_normal_sample_id']
     
     return_id=None

From c52a2d4b6b9c88b650b8ff2f6603362ec760d781 Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Mon, 26 Jun 2023 13:13:27 -0400
Subject: [PATCH 5/5] updated main.py

---
 sanity-check/main.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sanity-check/main.py b/sanity-check/main.py
index 881cf0c..5e58ada 100755
--- a/sanity-check/main.py
+++ b/sanity-check/main.py
@@ -152,10 +152,10 @@ def get_clinical(metadata,clinical_url,api_token):
 
     if return_metadata['tumour_normal_designation']=="Tumour":
         #WGS, WXS, RNA-Seq, Bisulfite-Seq, ChIP-Seq, Targeted-Seq
-        if metadata.get("experimental_strategy") in ['WGS', 'WXS']:
-            if metadata.get("submitter_matched_normal_sample_id"):
-                check_normal_sample_exists(metadata,response.json())
-            else:
+        if metadata.get("submitter_matched_normal_sample_id"):
+            check_normal_sample_exists(metadata,response.json())
+        else:
+            if metadata.get("experimental_strategy") in ['WGS', 'WXS']:
                 sys.exit("Null entry for `submitter_matched_normal_sample_id` detected. For tumour `experiment_strategy` type %s ,this field is required and must reference a registered normal sample." % (metadata.get("experimental_strategy")))
 
     return return_metadata