Feature/nextflow support (#6)

* basic nextflow workflow

* Updated travis and readme

Author: agduncan94

.travis.yml

@@ -6,6 +6,7 @@ services:
 env:
   - LANGUAGE=cwl
   - LANGUAGE=wdl
+  - LANGUAGE=nfl
 
 notifications:
   slack: 

README.md

@@ -102,4 +102,13 @@ $> dockstore tool wdl --entry quay.io/collaboratory/dockstore-tool-bamstats > Do
 $> 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
+```

install.sh

@@ -9,4 +9,7 @@ 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

@@ -9,4 +9,6 @@ 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