Merge pull request #1 from CancerCollaboratory/develop

This updates the fork with WDL and Nextflow versions of the tool

.travis.yml

@@ -3,6 +3,11 @@ sudo: required
 services:
   - docker
 
+env:
+  - LANGUAGE=cwl
+  - LANGUAGE=wdl
+  - LANGUAGE=nfl
+
 notifications:
   slack: 
     on_success: never
@@ -16,10 +21,10 @@ jdk:
 
 before_install:
   - docker build -t quay.io/collaboratory/dockstore-tool-bamstats .
-  - pip2.7 install --user setuptools==24.0.3
+  - bash before-install.sh
 
 install: 
-  - pip2.7 install --user cwl-runner cwltool==1.0.20160712154127 schema-salad==1.14.20160708181155 avro==1.8.1
+  - bash install.sh
 
 script: 
-  - cwltool --non-strict Dockstore.cwl test.json 
+  - bash script.sh

Dockstore.wdl

@@ -0,0 +1,27 @@
+task bamstats {
+	File bam_input
+	Int mem_gb
+
+	command {
+		bash /usr/local/bin/bamstats ${mem_gb} ${bam_input}
+	}
+
+	output {
+		File bamstats_report = "bamstats_report.zip"
+	}
+
+	runtime {
+		docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0" 
+		memory: mem_gb + "GB"
+	}
+
+	meta {
+		author: "Andrew Duncan"
+	}
+}
+
+workflow bamstatsWorkflow {
+	File bam_input
+	Int mem_gb	
+	call bamstats { input: bam_input=bam_input, mem_gb=mem_gb }
+}

README.md

@@ -43,9 +43,11 @@ You'll then see a file, `bamstats_report.zip`, in the current directory, that's
 ## Running Through the Dockstore CLI
 
 This tool can be found at the [Dockstore](https://dockstore.org), login with your GitHub account and follow the 
-directions to setup the CLI.  It lets you run a Docker container with a CWL descriptor locally, using Docker and the CWL command line utility.  This is great for testing.
+directions to setup the CLI.  It lets you run a Docker container with a CWL/WDL descriptor locally, using Docker and the CWL/WDL command line utility.  This is great for testing.
 
-### Make a Parameters JSON
+### With CWL
+
+#### Make a Parameters JSON
 
 This is the parameterization of the BAM stat tool, a copy is present in this repo called `sample_configs.json`:
 
@@ -62,7 +64,7 @@ This is the parameterization of the BAM stat tool, a copy is present in this rep
 }
 ```
 
-### Run with the CLI
+#### Run with the CLI
 
 Run it using the `dockstore` CLI:
 
@@ -76,4 +78,37 @@ $> dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
 $> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-3 --json Dockstore.json
 ```
 
+### With WDL
+#### Make a Parameters JSON
+
+This is the parameterization of the BAM stat tool, a copy is present in this repo called `test.wdl.json`:
+
+```
+{
+  "bamstatsWorkflow.bam_input": "rna.SRR948778.bam",
+  "bamstatsWorkflow.mem_gb": "4"
+}
+```
+
+#### Run with the CLI
+
+Run it using the `dockstore` CLI:
 
+```
+Usage:
+# fetch WDL
+$> dockstore tool wdl --entry quay.io/collaboratory/dockstore-tool-bamstats > Dockstore.wdl
+# make a runtime JSON template and edit it (or use the content of test.wdl.json above)
+$> dockstore tool convert wdl2json --wdl Dockstore.wdl > Dockstore.json
+# run it locally with the Dockstore CLI
+$> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats --json Dockstore.json
+```
+
+## Running Nextflow Workflow
+
+Install [Nextflow](https://www.nextflow.io/). Nextflow workflows cannot be run with the Dockstore CLI yet.
+
+The workflow can be run using the following command:
+```
+$> nextflow run main.nf
+```

before-install.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+
+if [[ "${LANGUAGE}" == "cwl" ]]; then
+    pip2.7 install --user setuptools==24.0.3
+fi

install.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+
+if [[ "${LANGUAGE}" == "cwl" ]]; then
+    pip2.7 install --user cwl-runner cwltool==1.0.20160712154127 schema-salad==1.14.20160708181155 avro==1.8.1
+elif [[ "${LANGUAGE}" == "wdl" ]]; then
+    wget https://github.com/broadinstitute/cromwell/releases/download/32/cromwell-32.jar
+elif [[ "${LANGUAGE}" == "nfl" ]]; then
+    curl -s https://get.nextflow.io | bash
+    mv nextflow $HOME/bin
+fi

main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+bamFile = file(params.bam_input)
+
+process bamstats {
+    input:
+    file bam_input from bamFile
+    val mem_gb from params.mem_gb
+
+    output:
+    file 'bamstats_report.zip'
+
+    """
+    bash /usr/local/bin/bamstats $mem_gb $bam_input
+    """
+}

nextflow.config

@@ -0,0 +1,15 @@
+manifest {
+    description = 'Generate some stats on a BAM file'
+    author = 'Andrew Duncan'
+}
+
+params {
+	bam_input = 'rna.SRR948778.bam'
+	mem_gb = '4'
+}
+
+process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-6_1.0'
+docker {
+    enabled = true
+    docker.runOptions = '-u $(id -u):$(id -g)'
+}

script.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o pipefail
+set -o nounset
+set -o xtrace
+
+if [[ "${LANGUAGE}" == "cwl" ]]; then
+    cwltool --non-strict Dockstore.cwl test.json
+elif [[ "${LANGUAGE}" == "wdl" ]]; then
+    java -jar cromwell-32.jar run Dockstore.wdl --inputs test.wdl.json
+elif [[ "${LANGUAGE}" == "nfl" ]]; then
+    nextflow run main.nf
+fi

test.wdl.json

@@ -0,0 +1,4 @@
+{
+  "bamstatsWorkflow.bam_input": "rna.SRR948778.bam",
+  "bamstatsWorkflow.mem_gb": "4"
+}