Merge pull request #124 from broadinstitute/dp-assembly

add run_discordance task

pipes/WDL/tasks/tasks_assembly.wdl

@@ -648,3 +648,70 @@ task refine_2x_and_plot {
         dx_instance_type: "mem1_ssd1_v2_x8"
     }
 }
+
+task run_discordance {
+    meta {
+      description: "This step evaluates discordance between sequencing runs of the same sample. The input is a merged, aligned BAM file for a single sample. If multiple runs (read groups) exist, we split the aligned reads by read group and separately evaluate consensus calls per read group using bcftools mpileup and call. A VCF is emitted that describes variation between runs."
+    }
+
+    input {
+      File     reads_aligned_bam
+      File     reference_fasta
+      String   out_basename = "run"
+
+      String   docker="quay.io/broadinstitute/viral-core"
+    }
+
+    command {
+        set -ex -o pipefail
+
+        read_utils.py --version | tee VERSION
+
+        # create 2-col table with read group ids in both cols
+        python3 <<CODE
+        import tools.samtools
+        header = tools.samtools.SamtoolsTool().getHeader("${reads_aligned_bam}")
+        rgids = [[x[3:] for x in h if x.startswith('ID:')][0] for h in header if h[0]=='@RG']
+        with open('readgroups.txt', 'wt') as outf:
+          for rg in rgids:
+            outf.write(rg+'\t'+rg+'\n')
+        CODE
+
+        # bcftools call snps while treating each RG as a separate sample
+        bcftools mpileup \
+          -G readgroups.txt -d 10000 -a "FORMAT/DP,FORMAT/AD" \
+          -q 1 -m 2 -Ou \
+          -f "${reference_fasta}" "${reads_aligned_bam}" \
+          | bcftools call \
+          -P 0 -m --ploidy 1 \
+          --threads $(nproc) \
+          -Ov -o everything.vcf
+
+        # mask all GT calls when less than 3 reads
+        cat everything.vcf | bcftools filter -e 'FMT/DP<3' -S . > filtered.vcf
+        cat filtered.vcf | bcftools filter -i 'MAC>0' > "${out_basename}.discordant.vcf"
+
+        # tally outputs
+        set +o pipefail # to handle empty grep
+        cat filtered.vcf | bcftools filter -i 'MAC=0' | grep -v '^#' | wc -l | tee num_concordant
+        cat "${out_basename}.discordant.vcf" | bcftools filter -i 'TYPE="snp"' | grep -v '^#' | wc -l | tee num_discordant_snps
+        cat "${out_basename}.discordant.vcf" | bcftools filter -i 'TYPE!="snp"' | grep -v '^#' | wc -l | tee num_discordant_indels
+    }
+
+    output {
+        File   discordant_sites_vcf = "${out_basename}.discordant.vcf"
+        Int    concordant_sites  = read_int("num_concordant")
+        Int    discordant_snps   = read_int("num_discordant_snps")
+        Int    discordant_indels = read_int("num_discordant_indels")
+        String viralngs_version  = read_string("VERSION")
+    }
+
+    runtime {
+        docker: "${docker}"
+        memory: "3 GB"
+        cpu: 2
+        disks: "local-disk 100 HDD"
+        dx_instance_type: "mem1_ssd1_v2_x2"
+        preemptible: 1
+    }
+}

pipes/WDL/tasks/tasks_reports.wdl

@@ -145,7 +145,6 @@ task align_and_count {
   input {
     File    reads_bam
     File    ref_db
-    Int?    minScoreToFilter
     Int?    topNHits = 3
 
     Int?    machine_mem_gb
@@ -161,11 +160,10 @@ task align_and_count {
     read_utils.py --version | tee VERSION
 
     ln -s ${reads_bam} ${reads_basename}.bam
-    read_utils.py bwamem_idxstats \
+    read_utils.py minimap2_idxstats \
       ${reads_basename}.bam \
       ${ref_db} \
       --outStats ${reads_basename}.count.${ref_basename}.txt.unsorted \
-      ${'--minScoreToFilter=' + minScoreToFilter} \
       --loglevel=DEBUG
 
       sort -b -r -n -k3 ${reads_basename}.count.${ref_basename}.txt.unsorted > ${reads_basename}.count.${ref_basename}.txt
@@ -179,7 +177,7 @@ task align_and_count {
   }
 
   runtime {
-    memory: select_first([machine_mem_gb, 7]) + " GB"
+    memory: select_first([machine_mem_gb, 3]) + " GB"
     cpu: 4
     docker: "${docker}"
     disks: "local-disk 375 LOCAL"
@@ -367,7 +365,7 @@ task tsv_join {
     String         join_type="inner"
     String         out_basename
 
-    String         docker="stratdat/csvkit"
+    String         docker="quay.io/broadinstitute/viral-core"
   }
 
   command {
@@ -408,7 +406,7 @@ task tsv_stack {
   input {
     Array[File]+   input_tsvs
     String         out_basename
-    String         docker="stratdat/csvkit"
+    String         docker="quay.io/broadinstitute/viral-core"
   }
 
   command {

pipes/WDL/workflows/assemble_refbased.wdl

@@ -94,6 +94,13 @@ workflow assemble_refbased {
             out_basename        = "${sample_name}.align_to_ref.trimmed"
     }
 
+    call assembly.run_discordance {
+        input:
+            reads_aligned_bam = merge_align_to_ref.out_bam,
+            reference_fasta   = reference_fasta,
+            out_basename      = sample_name
+    }
+
     call reports.plot_coverage as plot_ref_coverage {
         input:
             aligned_reads_bam   = merge_align_to_ref.out_bam,
@@ -140,6 +147,11 @@ workflow assemble_refbased {
         Int    reference_genome_length      = plot_ref_coverage.assembly_length
         Float  assembly_mean_coverage       = plot_ref_coverage.mean_coverage
 
+        Int    replicate_concordant_sites  = run_discordance.concordant_sites
+        Int    replicate_discordant_snps   = run_discordance.discordant_snps
+        Int    replicate_discordant_indels = run_discordance.discordant_indels
+        File   replicate_discordant_vcf    = run_discordance.discordant_sites_vcf
+
         Array[File]   align_to_ref_per_input_aligned_flagstat = align_to_ref.aligned_bam_flagstat
         Array[Int]    align_to_ref_per_input_reads_provided   = align_to_ref.reads_provided
         Array[Int]    align_to_ref_per_input_reads_aligned    = align_to_ref.reads_aligned

pipes/WDL/workflows/diff_genome_sets.wdl

@@ -21,7 +21,7 @@ workflow diff_genome_sets {
     call reports.tsv_stack {
         input:
             input_tsvs = compare_two_genomes.comparison_table,
-            out_basename = "diff_genome_sets.txt"
+            out_basename = "diff_genome_sets"
     }
 
     output {

requirements-modules.txt

@@ -1,7 +1,7 @@
-broadinstitute/viral-core=2.1.3
-broadinstitute/viral-assemble=2.1.3.1
-broadinstitute/viral-classify=2.1.3.1
-broadinstitute/viral-phylo=2.1.3.1
+broadinstitute/viral-core=2.1.4
+broadinstitute/viral-assemble=2.1.4.0
+broadinstitute/viral-classify=2.1.4.0
+broadinstitute/viral-phylo=2.1.4.0
 broadinstitute/beast-beagle-cuda=1.10.5pre
 broadinstitute/ncbi-tools=2.10.7.0
 nextstrain/base=build-20200608T223413Z

test/input/WDL/test_outputs-assemble_refbased-local.json

@@ -7,5 +7,7 @@
   "assemble_refbased.align_to_self_merged_reads_aligned": 18409,
   "assemble_refbased.reference_genome_length": 18959,
   "assemble_refbased.assembly_length_unambiguous": 18889,
-  "assemble_refbased.assembly_length": 18889
+  "assemble_refbased.assembly_length": 18889,
+  "assemble_refbased.replicate_discordant_indels": 0,
+  "assemble_refbased.replicate_discordant_snps": 0
 }