Test SRA workflow with cromwell

Author: Yan Xu

installation/install.sh

@@ -24,12 +24,32 @@ if [ ! -d  $io_home ]; then
     mkdir ${io_home}/${dir}
   done
 
-  test_data_home=$app_home/workflows/Nextflow/test_data
-  if [ -d  $test_data_home ]; then
-    ln -s ${test_data_home} ${io_home}/public/nextflow
+  cromwell_test_data_home=$app_home/workflows/Cromwell/test_data
+  if [ -d  $cromwell_test_data_home ]; then
+    ln -s ${cromwell_test_data_home} ${io_home}/public/cromwell
+  fi
+
+  nextflow_test_data_home=$app_home/workflows/Nextflow/test_data
+  if [ -d  $nextflow_test_data_home ]; then
+    ln -s ${nextflow_test_data_home} ${io_home}/public/nextflow
   fi
 fi
 
+echo "Generate Cromwell wdl imports.zip"
+wdl_dirs=(
+  "data"
+)
+
+for wdl_dir in "${wdl_dirs[@]}"
+do
+  cd $app_home/workflows/Cromwell/WDL/${wdl_dir}
+  zip -r imports.zip *.wdl
+  if [ "$?" != "0" ]; then
+    echo "Cannot create $app_home/workflows/Cromwell/WDL/${wdl_dir}/imports.zip!" 1>&2
+    exit 1
+  fi
+done
+
 echo "Setup LANL EDGE webapp ..."
 #build client
 echo "build client..."

webapp/client/src/edge/project/forms/TextInput.js

@@ -12,6 +12,7 @@ export const TextInput = (props) => {
 
   const {
     register,
+    reset,
     formState: { errors },
     trigger,
   } = useForm({
@@ -54,6 +55,15 @@ export const TextInput = (props) => {
     }
   }, []) // eslint-disable-line react-hooks/exhaustive-deps
 
+  useEffect(() => {
+    if (props.defaultValue) {
+      reset({ textInput: props.defaultValue })
+    } else {
+      reset({ textInput: '' })
+    }
+    setDoValidation(doValidation + 1)
+  }, [props.reset]) // eslint-disable-line react-hooks/exhaustive-deps
+
   useEffect(() => {
     //validate form
     trigger().then((result) => {

webapp/server/utils/cromwell.js

@@ -24,7 +24,7 @@ const generateInputs = async (projHome, projectConf, workflowConf) => {
   // projectConf: project conf.js
   // workflowList in utils/workflow
   const workflowSettings = workflowList[projectConf.workflow.name];
-  const template = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.inputs_tmpl}`));
+  const template = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.inputs_tmpl}`));
   const params = { ...workflowConf, ...projectConf.workflow.input, outdir: `${projHome}/${workflowSettings.outdir}` };
 
   if (projectConf.workflow.name === 'sra2fastq') {
@@ -35,8 +35,8 @@ const generateInputs = async (projHome, projectConf, workflowConf) => {
   const inputs = ejs.render(template, params);
   await fs.promises.writeFile(`${projHome}/pipeline_inputs.json`, inputs);
   // render options template and write to pipeline_options.json
-  if (fs.existsSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.options_tmpl}`)) {
-    const optionsTemplate = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${projectConf.category}/${workflowSettings.options_tmpl}`));
+  if (fs.existsSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.options_tmpl}`)) {
+    const optionsTemplate = String(fs.readFileSync(`${config.CROMWELL.TEMPLATE_DIR}/${workflowSettings.options_tmpl}`));
     const options = ejs.render(optionsTemplate, params);
     await fs.promises.writeFile(`${projHome}/pipeline_options.json`, options);
   }
@@ -52,7 +52,7 @@ const submitWorkflow = (proj, projectConf, inputsize) => {
   formData.append('workflowInputs', fs.createReadStream(`${projHome}/pipeline_inputs.json`));
   // logger.debug(`workflowInputs${projHome}/pipeline_inputs.json`);
 
-  const imports = `${config.CROMWELL.WDL_DIR}/${projectConf.category}/${workflowList[projectConf.workflow.name].wdl_imports}`;
+  const imports = `${config.CROMWELL.WDL_DIR}/${workflowList[projectConf.workflow.name].wdl_imports}`;
   const optionsJson = `${projHome}/pipeline_options.json`;
 
   if (fs.existsSync(optionsJson)) {

webapp/server/utils/workflow.js

@@ -12,8 +12,8 @@ const nextflowConfigs = {
 const workflowList = {
   default_wdl_version: '1.0',
   sra2fastq: {
-    wdl: 'sra2fastq.wdl',
-    wdl_imports: 'imports.zip',
+    wdl: 'data/sra2fastq.wdl',
+    wdl_imports: 'data/imports.zip',
     inputs_tmpl: 'data/sra2fastq_inputs.tmpl',
     cromwell_calls: ['sra.sra2fastq'],
     outdir: 'output/sra2fastq',