Add user error for insufficient coverage

consensus-genome/Dockerfile

@@ -53,8 +53,8 @@ RUN apt-get -qq update && apt-get -qq -y install \
 # These newer versions of infernal and ncbi-blast+ are required by VADR
 RUN curl -O -L https://ftp.osuosl.org/pub/ubuntu/pool/universe/i/infernal/infernal_1.1.4-1_amd64.deb && \
   dpkg -i infernal_1.1.4-1_amd64.deb && \
-  curl -O -L https://ftp.osuosl.org/pub/ubuntu/pool/universe/n/ncbi-blast+/ncbi-blast+_2.10.1-2_amd64.deb && \
-  dpkg -i ncbi-blast+_2.10.1-2_amd64.deb
+  curl -O -L https://ftp.osuosl.org/pub/ubuntu/pool/universe/n/ncbi-blast+/ncbi-blast+_2.10.1+ds-1_amd64.deb && \
+  dpkg -i ncbi-blast+_2.10.1+ds-1_amd64.deb
 
 # See https://github.com/ablab/quast/issues/157
 RUN pip3 install multiqc==1.8 quast==5.0.2 && \

consensus-genome/run.wdl

@@ -897,18 +897,20 @@ task ComputeStats {
         import json
         import re
         import pysam
+        import sys
         from Bio import SeqIO
         import numpy as np
         from matplotlib import pyplot as plt
         import seaborn as sns
-
+
+        error = lambda err, cause: sys.exit(json.dumps(dict(wdl_error_message=True, error=err, cause=cause)))
         stats = {"sample_name": "~{sample}"}
 
         depths = open("~{prefix}samtools_depth.txt").read().splitlines()
         if depths:
             depths = np.array([int(d) for d in depths])
         else:
-            raise Exception("Insufficient coverage to proceed with CG analysis")
+            error("InsufficientReadsError", "Insufficient coverage to proceed with CG analysis")
 
         stats["depth_avg"] = depths.mean()
         stats["depth_q.25"] = np.quantile(depths, .25)

consensus-genome/test/test_wdl.py

@@ -168,6 +168,27 @@ def test_fetch_sequence_by_expired_accession_id(self):
         self.assertRunFailed(ecm, task="FetchSequenceByAccessionId",
                              error="AccessionIdNotFound", cause="Accession ID NO_ACCESSION_ID not found in the index")
 
+    def test_no_coverage_error(self):
+        ref_host_blank = os.path.join(os.path.dirname(__file__), "blank.fastq.gz")
+        assembly_blank = os.path.join(os.path.dirname(__file__), "blank.fastq.gz")
+        vcf_blank = os.path.join(os.path.dirname(__file__), "blank.fastq.gz")
+        fastqs_blank = os.path.join(os.path.dirname(__file__), "blank.fastq.gz")
+        cleaned_bam = os.path.join(os.path.dirname(__file__), "empty.bam")
+        with self.assertRaises(CalledProcessError) as ecm:
+            self.run_miniwdl(task="ComputeStats", args=[
+                f"ref_host={ref_host_blank}",
+                f"assembly={assembly_blank}",
+                f"vcf={vcf_blank}",
+                f"fastqs={fastqs_blank}",
+                "technology=Illumina",
+                f"cleaned_bam={cleaned_bam}"],
+                task_input={
+                    "sample": "sample",
+                    "prefix": "",
+                })
+        self.assertRunFailed(ecm, task="ComputeStats",
+                             error="InsufficientReadsError", cause="Insufficient coverage to proceed with CG analysis")
+
     def test_max_reads_illumina(self):
         fastq_0 = os.path.join(os.path.dirname(__file__), "SRR11741455_65054_nh_R1.fastq.gz")
         fastq_1 = os.path.join(os.path.dirname(__file__), "SRR11741455_65054_nh_R2.fastq.gz")

short-read-mngs/test/postprocess/test_RunAssembly.py

@@ -10,10 +10,10 @@ def test_RunAssembly_defaults(util, short_read_mngs_bench3_viral_outputs):
     min_contig_length filter)
     """
     assembly_contigs_fasta = short_read_mngs_bench3_viral_outputs["outputs"][
-        "idseq_short_read_mngs.postprocess.assembly_out_assembly_contigs_fasta"
+        "czid_short_read_mngs.postprocess.assembly_out_assembly_contigs_fasta"
     ]
     assembly_contigs_all_fasta = short_read_mngs_bench3_viral_outputs["outputs"][
-        "idseq_short_read_mngs.postprocess.assembly_out_assembly_contigs_all_fasta"
+        "czid_short_read_mngs.postprocess.assembly_out_assembly_contigs_all_fasta"
     ]
     assembly_contigs = list(SeqIO.parse(assembly_contigs_fasta, "fasta"))
     assembly_contigs_all = list(SeqIO.parse(assembly_contigs_all_fasta, "fasta"))