deal with missing lane index (#165)

adapter_pipelines/Optimus/adapter.wdl

@@ -138,7 +138,7 @@ workflow AdapterOptimus {
   Boolean record_http = false
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.4"
+  String pipeline_tools_version = "v0.56.5"
 
   call GetInputs as prep {
     input:

adapter_pipelines/cellranger/adapter.wdl

@@ -148,7 +148,7 @@ workflow Adapter10xCount {
   Boolean record_http = false
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.4"
+  String pipeline_tools_version = "v0.56.5"
 
   call GetInputs {
     input:

adapter_pipelines/ss2_single_end/adapter.wdl

@@ -69,7 +69,7 @@ workflow AdapterSmartSeq2SingleCellUnpaired {
   Boolean record_http = false
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.4"
+  String pipeline_tools_version = "v0.56.5"
 
   call GetInputs as prep {
     input:

adapter_pipelines/ss2_single_sample/adapter.wdl

@@ -69,7 +69,7 @@ workflow AdapterSmartSeq2SingleCell{
   Boolean record_http = false
   Boolean add_md5s = false
 
-  String pipeline_tools_version = "v0.56.4"
+  String pipeline_tools_version = "v0.56.5"
 
   call GetInputs as prep {
     input:

pipeline_tools/shared/tenx_utils.py

@@ -29,7 +29,15 @@ def create_fastq_dict(fastq_files):
     lane_to_fastqs = {}
     for file in fastq_files:
         lane = file.lane_index
-        if lane not in lane_to_fastqs:
+        if lane is None:
+            lane = 0
+        if lane in lane_to_fastqs:
+            if file.read_index in lane_to_fastqs[lane]:
+                raise InsufficientLaneInfoError(
+                    'There are multiple sets of reads, but no lane index. '
+                    'Cannot properly group reads for analysis.'
+                )
+        else:
             lane_to_fastqs[lane] = {}
         lane_to_fastqs[lane][file.read_index] = file.manifest_entry
 
@@ -132,3 +140,7 @@ def validate_lanes(lane_to_fastqs):
 
 class LaneMissingFileError(Exception):
     pass
+
+
+class InsufficientLaneInfoError(Exception):
+    pass

pipeline_tools/tests/shared/test_tenx_utils.py

@@ -108,6 +108,49 @@ def invalid_files_missing_read2():
     return files
 
 
+@pytest.fixture
+def missing_lane_index_one_set_of_reads():
+    files = [
+        BundleFile(
+            'fastq.gz', None, 'read1', ManifestEntry('gs://somewhere/r1.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'read2', ManifestEntry('gs://somewhere/r2.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'index1', ManifestEntry('gs://somewhere/i1.fastq.gz')
+        ),
+    ]
+    r.shuffle(files)
+    return files
+
+
+@pytest.fixture
+def missing_lane_index_multiple_sets_of_reads():
+    files = [
+        BundleFile(
+            'fastq.gz', None, 'read1', ManifestEntry('gs://somewhere/r1.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'read2', ManifestEntry('gs://somewhere/r2.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'index1', ManifestEntry('gs://somewhere/i1.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'read1', ManifestEntry('gs://somewhereelse/r1.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'read2', ManifestEntry('gs://somewhereelse/r2.fastq.gz')
+        ),
+        BundleFile(
+            'fastq.gz', None, 'index1', ManifestEntry('gs://somewhereelse/i1.fastq.gz')
+        ),
+    ]
+    r.shuffle(files)
+    return files
+
+
 def test_create_fastq_dict(
     valid_files_with_index,
     valid_files_with_index_dict,
@@ -151,6 +194,19 @@ def test_validate_lanes_accepts_lanes_when_none_indexed(valid_files_no_index):
     tenx_utils.validate_lanes(fastq_dict)
 
 
+def test_create_fastq_dict_reindexes_with_zero_when(
+    missing_lane_index_one_set_of_reads
+):
+    fastq_dict = tenx_utils.create_fastq_dict(missing_lane_index_one_set_of_reads)
+    assert 0 in fastq_dict
+    assert None not in fastq_dict
+
+
+def test_create_fastq_dict_raises_error_when(missing_lane_index_multiple_sets_of_reads):
+    with pytest.raises(tenx_utils.InsufficientLaneInfoError):
+        tenx_utils.create_fastq_dict(missing_lane_index_multiple_sets_of_reads)
+
+
 def test_get_fastqs_for_read_index(valid_files_with_index):
     fastq_dict = tenx_utils.create_fastq_dict(valid_files_with_index)
     fastqs = tenx_utils.get_fastqs_for_read_index(fastq_dict, 'read1')