From 8f705829f8922b840a0190b05042a7898cde9765 Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Wed, 5 Feb 2020 16:53:50 -0500
Subject: [PATCH 1/2] add fastq_to_bam wdl task and workflow

add fastq_to_bam wdl task and workflow to call read_utils.py::fastq_to_bam
---
 pipes/WDL/workflows/fastq_to_bam.wdl          |  5 ++++
 .../WDL/workflows/tasks/tasks_read_utils.wdl  | 29 +++++++++++++++++++
 2 files changed, 34 insertions(+)
 create mode 100644 pipes/WDL/workflows/fastq_to_bam.wdl

diff --git a/pipes/WDL/workflows/fastq_to_bam.wdl b/pipes/WDL/workflows/fastq_to_bam.wdl
new file mode 100644
index 000000000..c628761df
--- /dev/null
+++ b/pipes/WDL/workflows/fastq_to_bam.wdl
@@ -0,0 +1,5 @@
+import "tasks_read_utils.wdl" as read_utils
+
+workflow paired_fastqs_to_bam {
+    call read_utils.fastq_to_bam
+}
diff --git a/pipes/WDL/workflows/tasks/tasks_read_utils.wdl b/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
index 90f39d8f0..13dd953fd 100644
--- a/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
+++ b/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
@@ -37,4 +37,33 @@ task downsample_bams {
   }
 }
 
+task fastq_to_bam {
+  File  in_fastq1
+  File  in_fastq2
+  #File? header
 
+  # also used for outfile name
+  String? sample_name = basename(basename(basename(basename(basename(basename(in_fastq1, ".1.fastq"),".1.fq"),".fastq"),".fq"),".fq1"),".fastq1")
+
+  command {
+    read_utils.py fastq_to_bam \
+        ${in_fastq1} \
+        ${in_fastq2} \
+        ${sample_name}.bam \
+        ${'--sampleName=' + sample_name} \
+        #${'--header ' + header} \
+        --JVMmemory "1g"
+  }
+
+  output {
+    File out_bam            = "${sample_name}.bam"
+    String viralngs_version = "viral-ngs_version_unknown"
+  }
+  runtime {
+    docker: "quay.io/broadinstitute/viral-ngs"
+    memory: "3 GB"
+    cpu: 2
+    dx_instance_type: "mem1_ssd1_v2_x4"
+    preemptible: 0
+  }
+}

From 85b9faa035feb9b2a61ad0f9df93a24c71cab41e Mon Sep 17 00:00:00 2001
From: Christopher Tomkins-Tinch <tomkinsc@broadinstitute.org>
Date: Fri, 20 Mar 2020 12:52:09 -0400
Subject: [PATCH 2/2] uncomment header param

---
 pipes/WDL/workflows/tasks/tasks_read_utils.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pipes/WDL/workflows/tasks/tasks_read_utils.wdl b/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
index 13dd953fd..bc5276f07 100644
--- a/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
+++ b/pipes/WDL/workflows/tasks/tasks_read_utils.wdl
@@ -40,7 +40,7 @@ task downsample_bams {
 task fastq_to_bam {
   File  in_fastq1
   File  in_fastq2
-  #File? header
+  File? header
 
   # also used for outfile name
   String? sample_name = basename(basename(basename(basename(basename(basename(in_fastq1, ".1.fastq"),".1.fq"),".fastq"),".fq"),".fq1"),".fastq1")
@@ -51,7 +51,7 @@ task fastq_to_bam {
         ${in_fastq2} \
         ${sample_name}.bam \
         ${'--sampleName=' + sample_name} \
-        #${'--header ' + header} \
+        ${'--header ' + header} \
         --JVMmemory "1g"
   }