Merge pull request #280 from microbiomedata/279-duplicate-fastq-inputs

Remove duplicate fastqs from inputs
microbiomedata · Aug 19, 2024 · e211e5a · e211e5a
2 parents 831d1fa + 7e964e5
commit e211e5a
Showing 1 changed file with 10 additions and 6 deletions.
diff --git a/webapp/server/crons/pipelineMonitor.js b/webapp/server/crons/pipelineMonitor.js
@@ -163,10 +163,10 @@ async function generateInputs(proj_home, conf, proj) {
                 const fileCode = path.basename(fq);
                 let name = await common.getRealName(fileCode);
                 const inputFq = inputDir + "/" + name;
-                if(!fs.existsSync(inputFq)) {
+                if (!fs.existsSync(inputFq)) {
                     fs.symlinkSync(fq, inputFq, 'file');
+                    inputs.push(inputFq);
                 }
-                inputs.push(inputFq);
             } else {
                 inputs.push(fq);
             }
@@ -191,8 +191,10 @@ async function generateInputs(proj_home, conf, proj) {
                 const fileCode = path.basename(fq1);
                 let name = await common.getRealName(fileCode);
                 const inputFq = inputDir + "/" + name;
-                fs.symlinkSync(fq1, inputFq, 'file');
-                inputs_fq1.push(inputFq);
+                if (!fs.existsSync(inputFq)) {
+                    fs.symlinkSync(fq1, inputFq, 'file');
+                    inputs_fq1.push(inputFq);
+                }
             } else {
                 inputs_fq1.push(fq1);
             }
@@ -206,8 +208,10 @@ async function generateInputs(proj_home, conf, proj) {
                 const fileCode = path.basename(fq2);
                 let name = await common.getRealName(fileCode);
                 const inputFq = inputDir + "/" + name;
-                fs.symlinkSync(fq2, inputFq, 'file');
-                inputs_fq2.push(inputFq);
+                if (!fs.existsSync(inputFq)) {
+                    fs.symlinkSync(fq2, inputFq, 'file');
+                    inputs_fq2.push(inputFq);
+                }
             } else {
                 inputs_fq2.push(fq2);
             }