update Dockerfile and Makefile for Canu version update. add parameter in Canu.wdl.

docker/lr-canu/Dockerfile

@@ -1,9 +1,12 @@
 FROM openjdk:8
 
 RUN apt-get update && \
-    apt-get install libgomp1
+    apt-get install libgomp1 tree
 
-RUN wget https://github.com/marbl/canu/releases/download/v2.0/canu-2.0.Linux-amd64.tar.xz && \
-    tar -xvf canu-2.0.Linux-amd64.tar.xz
 
-ENV PATH="/canu-2.0/Linux-amd64/bin:${PATH}"
+RUN wget https://github.com/marbl/canu/releases/download/v2.2/canu-2.2.Linux-amd64.tar.xz && \
+    tar -xJf canu-2.2.*.tar.xz
+
+
+ENV PATH="/canu-2.2/bin:${PATH}"
+RUN canu

docker/lr-canu/Makefile

@@ -1,17 +1,15 @@
-IMAGE_NAME = lr-canu
-VERSION = 0.1.0
 
-TAG1 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):$(VERSION)
-TAG2 = us.gcr.io/broad-dsp-lrma/$(IMAGE_NAME):latest
+VERSION = 0.2.0
+
+TAG1 = us.gcr.io/broad-dsp-lrma/lr-canu:$(VERSION)
+TAG2 = us.gcr.io/broad-dsp-lrma/lr-canu:latest
+
 
 all: | build push
 
 build:
-    docker build -t $(TAG1) -t $(TAG2) .
-
-build_no_cache:
-    docker build --no-cache -t $(TAG1) -t $(TAG2) .
+	docker build -t $(TAG1) -t $(TAG2) .
 
 push:
-    docker push $(TAG1)
-    docker push $(TAG2)
+	docker push $(TAG1)
+	docker push $(TAG2)

wdl/tasks/Canu.wdl

@@ -4,29 +4,31 @@ version 1.0
 # A workflow that runs the Canu 3-step assembly (correct, trim, assemble).
 # - Tested on a small genome (malaria ~23mb), larger genomes may require some changes
 #     including tweaks to the default resource allocation.
-# - Currently assumes nanopore reads
+
 ##########################################################################################
 
 import "Structs.wdl"
 
 workflow Canu {
     input {
         File reads
-
+        String technology
         Int genome_size
         Float correct_error_rate
         Float trim_error_rate
         Float assemble_error_rate
-
         String prefix
+        Int corrected_coverage
     }
 
     call Correct {
         input:
             reads = reads,
+            corrected_coverage = corrected_coverage,
             genome_size = genome_size,
             error_rate = correct_error_rate,
-            prefix = prefix
+            prefix = prefix,
+            technology = technology
     }
 
     call Trim {
@@ -35,6 +37,7 @@ workflow Canu {
             corrected_reads = Correct.corrected_reads,
             error_rate = trim_error_rate,
             prefix = prefix,
+            technology = technology
     }
 
     call Assemble {
@@ -43,21 +46,24 @@ workflow Canu {
             trimmed_reads = Trim.trimmed_reads,
             error_rate = assemble_error_rate,
             prefix = prefix,
+            technology = technology
     }
 
     output {
         File fa = Assemble.canu_contigs_fasta
+        File log = Assemble.intermediate_log
     }
 }
 
-# performs canu correct on raw reads, currently assumes ONT reads
+# performs canu correct on raw reads
 task Correct {
     input {
         File reads
         Int genome_size
+        Int corrected_coverage
         Float error_rate
         String prefix
-
+        String technology
         RuntimeAttr? runtime_attr_override
     }
 
@@ -66,24 +72,28 @@ task Correct {
         genome_size:  "estimate on genome size (parameter to canu's 'genomeSize')"
         error_rate:   "parameter to canu's 'correctedErrorRate'"
         prefix:       "prefix to output files"
+        technology:   "sequencing technology (nanopore or pacbio)"
     }
 
+    String tech_specific_arg = if technology == 'ont' then "nanopore" else 'pacbio'
     Int disk_size = 150 * ceil(size(reads, "GB"))
 
     command <<<
         set -euxo pipefail
 
-        canu -correct \
+        canu -correct corOutCoverage=~{corrected_coverage}\
              -p ~{prefix} -d canu_correct_output \
-             genomeSize=~{genome_size}m \
+             genomeSize=~{genome_size}k \
              corMaxEvidenceErate=0.15 \
              correctedErrorRate=~{error_rate} \
-             -nanopore \
+             -~{tech_specific_arg} \
              ~{reads}
+        tree > intermediate.log
     >>>
 
     output {
         File corrected_reads = "canu_correct_output/~{prefix}.correctedReads.fasta.gz"
+        File intermediate_log = "intermediate.log"
     }
 
     #########################
@@ -94,7 +104,7 @@ task Correct {
         boot_disk_gb:       10,
         preemptible_tries:  0,
         max_retries:        0,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.1.0"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.2.0"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
@@ -115,6 +125,7 @@ task Trim {
         Int genome_size
         Float error_rate
         String prefix
+        String technology
 
         RuntimeAttr? runtime_attr_override
     }
@@ -124,23 +135,26 @@ task Trim {
         genome_size:       "estimate on genome size (parameter to canu's 'genomeSize')"
         corrected_reads:   "parameter to canu's 'correctedErrorRate'"
         prefix:            "prefix to output files"
+        technology:        "sequencing technology (nanopore or pacbio)"
     }
-
+    String tech_specific_arg = if technology == 'ont' then "nanopore" else 'pacbio'
     Int disk_size = 50 * ceil(size(corrected_reads, "GB"))
 
     command <<<
        set -euxo pipefail
 
        canu -trim \
             -p ~{prefix} -d canu_trim_output \
-            genomeSize=~{genome_size}m \
+            genomeSize=~{genome_size}k \
             correctedErrorRate=~{error_rate} \
-            -nanopore-corrected \
+            -~{tech_specific_arg}-corrected \
             ~{corrected_reads}
+        tree > intermediate.log
     >>>
 
     output {
         File trimmed_reads = "canu_trim_output/~{prefix}.trimmedReads.fasta.gz"
+        File intermediate_log = "intermediate.log"
     }
 
     #########################
@@ -151,7 +165,7 @@ task Trim {
         boot_disk_gb:       10,
         preemptible_tries:  0,
         max_retries:        0,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.1.0"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.2.0"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {
@@ -172,7 +186,7 @@ task Assemble {
         File trimmed_reads
         Float error_rate
         String prefix
-
+        String technology
         RuntimeAttr? runtime_attr_override
     }
 
@@ -181,34 +195,38 @@ task Assemble {
         genome_size:    "estimate on genome size (parameter to canu's 'genomeSize')"
         error_rate:     "parameter to canu's 'correctedErrorRate'"
         prefix:         "prefix to output files"
+        technology:     "sequencing technology (nanopore or pacbio)"
     }
 
+    String tech_specific_arg = if technology == 'ont' then "nanopore" else 'pacbio'
     Int disk_size = 50 * ceil(size(trimmed_reads, "GB"))
 
     command <<<
         set -euxo pipefail
 
         canu -assemble \
              -p ~{prefix} -d canu_assemble_output \
-             genomeSize=~{genome_size}m \
+             genomeSize=~{genome_size}k \
              correctedErrorRate=~{error_rate} \
-             -nanopore-corrected \
+             -~{tech_specific_arg}-corrected \
              ~{trimmed_reads}
+        tree > intermediate.log
     >>>
 
     output {
         File canu_contigs_fasta = "canu_assemble_output/~{prefix}.contigs.fasta"
+        File intermediate_log = "intermediate.log"
     }
 
     #########################
     RuntimeAttr default_attr = object {
         cpu_cores:          32,
-        mem_gb:             32,
+        mem_gb:             60,
         disk_gb:            disk_size,
-        boot_disk_gb:       10,
+        boot_disk_gb:       20,
         preemptible_tries:  0,
         max_retries:        0,
-        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.1.0"
+        docker:             "us.gcr.io/broad-dsp-lrma/lr-canu:0.2.0"
     }
     RuntimeAttr runtime_attr = select_first([runtime_attr_override, default_attr])
     runtime {