add check for no crams provided and add bp for rp buckets

Author: mmorgantaylor

pipelines/wdl/glimpse/low_pass_imputation/input_qc/Glimpse2LowPassImputationQC.wdl

@@ -201,8 +201,8 @@ task ValidateCramsAndIndicesAndSampleIds {
         num_cram_indices = len(cram_indices)
         num_sample_ids = len(sample_ids)
 
-        max_cram_file_size_gb = ~{max_cram_file_size_gb}
-        billing_project = "~{billing_project_for_rp}"
+        if num_crams == 0:
+            qc_messages.append("No CRAM files provided.")
 
         # Validate that the number of CRAMs, CRAIs, and sample IDs match
         if num_crams != num_cram_indices or num_crams != num_sample_ids:
@@ -240,14 +240,13 @@ task ValidateCramsAndIndicesAndSampleIds {
             print("CRAM paths are unique.")
 
         # Ensure that all CRAM files are less than the maximum file size allowed
+        max_cram_file_size_gb = ~{max_cram_file_size_gb}
+        billing_project = "~{billing_project_for_rp}"
         crams_exceeding_max_size = []
 
-        # Create storage client
         client = storage.Client(project=billing_project) if billing_project else storage.Client()
-
         for cram in crams:
             try:
-                # Parse GCS path: gs://bucket-name/path/to/file.cram
                 if cram.startswith('gs://'):
                     blob = storage.Blob.from_uri(cram, client=client)
                     
@@ -257,6 +256,7 @@ task ValidateCramsAndIndicesAndSampleIds {
                     # Get file size
                     file_size_bytes = blob.size
                     file_size_gb = file_size_bytes // (1024 ** 3)
+                    print(f" - File size for {cram}: {file_size_gb} GB")
                     
                     if file_size_gb > max_cram_file_size_gb:
                         crams_exceeding_max_size.append(f"{cram} ({file_size_gb}GB)")

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_cram_duplicate_cram_paths.json

@@ -7,5 +7,6 @@
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram"],
   "Glimpse2LowPassImputationQC.cram_indices": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai"],
-  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample1"]
+  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample1"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_cram_duplicate_sample_ids_and_duplicate_cram_paths.json

@@ -7,5 +7,6 @@
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram"],
   "Glimpse2LowPassImputationQC.cram_indices": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram.crai"],
-  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample0", "sample1", "sample1"]
+  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample0", "sample1", "sample1"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_cram_mismatched_array_lengths.json

@@ -7,5 +7,6 @@
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram"],
   "Glimpse2LowPassImputationQC.cram_indices": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram.crai"],
-  "Glimpse2LowPassImputationQC.sample_ids": ["sample0"]
+  "Glimpse2LowPassImputationQC.sample_ids": ["sample0"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_cram_no_crai.json

@@ -6,5 +6,6 @@
   "Glimpse2LowPassImputationQC.output_basename": "plumbing_test_fail_cram_without_crai",
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fake-bucket/fake-file1.cram", "gs://fake-bucket/fake-file2.cram"],
-  "Glimpse2LowPassImputationQC.sample_ids": ["sample1", "sample2"]
+  "Glimpse2LowPassImputationQC.sample_ids": ["sample1", "sample2"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_cram_no_sample_ids.json

@@ -6,5 +6,6 @@
   "Glimpse2LowPassImputationQC.output_basename": "plumbing_test_fail_cram_without_sample_ids",
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fake-bucket/fake-file1.cram", "gs://fake-bucket/fake-file2.cram"],
-  "Glimpse2LowPassImputationQC.cram_indices": ["gs://fake-bucket/fake-file1.crai", "gs://fake-bucket/fake-file2.crai"]
+  "Glimpse2LowPassImputationQC.cram_indices": ["gs://fake-bucket/fake-file1.crai", "gs://fake-bucket/fake-file2.crai"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/fail_manifest_duplicate_sample_ids.json

@@ -5,5 +5,6 @@
   "Glimpse2LowPassImputationQC.fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "Glimpse2LowPassImputationQC.output_basename": "plumbing_test",
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-  "Glimpse2LowPassImputationQC.cram_manifest": "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCramManifestDuplicateSamples.tsv"
+  "Glimpse2LowPassImputationQC.cram_manifest": "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCramManifestDuplicateSamples.tsv",
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/pass_cram.json

@@ -7,5 +7,6 @@
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
   "Glimpse2LowPassImputationQC.crams": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram"],
   "Glimpse2LowPassImputationQC.cram_indices": ["gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram0.cram.crai", "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCram1.cram.crai"],
-  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample1"]
+  "Glimpse2LowPassImputationQC.sample_ids": ["sample0", "sample1"],
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }

pipelines/wdl/glimpse/low_pass_imputation/input_qc/test_inputs/Plumbing/pass_manifest.json

@@ -5,5 +5,6 @@
   "Glimpse2LowPassImputationQC.fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
   "Glimpse2LowPassImputationQC.output_basename": "plumbing_test",
   "Glimpse2LowPassImputationQC.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
-  "Glimpse2LowPassImputationQC.cram_manifest": "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCramManifest.tsv"
+  "Glimpse2LowPassImputationQC.cram_manifest": "gs://fc-cddd72b5-323c-495c-9557-5057fff0275a/morgan_test/fakeCramManifest.tsv",
+  "Glimpse2LowPassImputationQC.billing_project_for_rp": "terra-f8e3de20"
 }