Merge pull request #21 from icgc-argo/validate-seqtools@0.1.3

[release]
icgc-argo · Aug 18, 2022 · f40f6ba · f40f6ba
2 parents 3c45343 + dc3dae5
commit f40f6ba
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 5 deletions.
diff --git a/validate-seqtools/main.nf b/validate-seqtools/main.nf
@@ -18,13 +18,14 @@
 
   Authors:
     Edmund Su
+    Linda Xiang
 */
 
 /********************************************************************/
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'
@@ -62,6 +63,7 @@ process validateSeqtools {
 
   output:  // output, make update as needed
     path "validation_report.*.jsonl", emit: validation_log
+    path "local_copy", emit: validated_payload
 
   script:
     // add and initialize variables here as needed
@@ -72,8 +74,14 @@ process validateSeqtools {
       -j local_copy \
       ${args_skip_md5sum_check} \
       > seq-tools.log 2>&1
-    rm local_copy
-    ls validation_report.PASS*.jsonl && ( exit 0 || exit 1)
+
+    if ls validation_report.INVALID*.jsonl 1> /dev/null 2>&1; then     
+      echo "Payload is INVALID. Please check out details in validation report under: "
+      pwd 
+      exit 1
+    else
+      exit 0
+    fi
     """
 }
 

diff --git a/validate-seqtools/pkg.json b/validate-seqtools/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "validate-seqtools",
-    "version": "0.1.2",
+    "version": "0.1.3",
     "description": "Using Seq-tools, validates molecular",
     "main": "main.nf",
     "deprecated": false,

diff --git a/validate-seqtools/tests/checker.nf b/validate-seqtools/tests/checker.nf
@@ -29,7 +29,7 @@
 /* this block is auto-generated based on info from pkg.json where   */
 /* changes can be made if needed, do NOT modify this block manually */
 nextflow.enable.dsl = 2
-version = '0.1.2'
+version = '0.1.3'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'