Merge pull request #15 from icgc-argo/validate-seqtools@0.1.1

[release]
icgc-argo · Aug 17, 2022 · f1e3957 · f1e3957
2 parents 4b2788a + e4156c1
commit f1e3957
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Showing 4 changed files with 7 additions and 4 deletions.
diff --git a/validate-seqtools/main.nf b/validate-seqtools/main.nf
@@ -24,7 +24,7 @@
 /* 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 = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'
@@ -67,10 +67,13 @@ process validateSeqtools {
     // add and initialize variables here as needed
     args_skip_md5sum_check = params.skip_md5sum_check  ? "--skip_md5sum_check " : ""
     """
+    cp ${json_file} local_copy
     python3 /tools/main.py \
-      -j ${json_file} \
+      -j local_copy \
       ${args_skip_md5sum_check} \
       > seq-tools.log 2>&1
+    rm local_copy
+    ls validation_report.PASS*.jsonl && ( exit 0 || exit 1)
     """
 }
 

diff --git a/validate-seqtools/pkg.json b/validate-seqtools/pkg.json
@@ -1,6 +1,6 @@
 {
     "name": "validate-seqtools",
-    "version": "0.1.0",
+    "version": "0.1.1",
     "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 = '0.1.0'  // package version
+version = '0.1.1'
 
 container = [
     'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools'

diff --git a/validate-seqtools/tests/test-job-fq.json → ...ate-seqtools/tests/local-test-job-fq.json b/validate-seqtools/tests/test-job-fq.json → ...ate-seqtools/tests/local-test-job-fq.json