Display message when error 132 found (#6675)

* Display message when error 132 found * Update snapshots * Make lint happy * Add call to the function with trap * Make nf-core lint happy * More linting * Make lint happy
nf-core · Sep 20, 2024 · 49057d3 · 49057d3
1 parent 1960623
commit 49057d3
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Showing 3 changed files with 28 additions and 8 deletions.
diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf
@@ -23,6 +23,18 @@ process KALIGN_ALIGN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def write_output = compress ? ">(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "${prefix}.aln"
     """
+    error_handler() {
+    exit_code=\$?
+        if [ \$exit_code -eq 132 ]; then
+            echo "\n\nKALIGN failed because is incompatible with some CPU types, see https://github.com/TimoLassmann/kalign/issues/46.\n\n"
+        else
+            trap - ERR
+            return \$exit_code
+        fi
+    }
+
+    trap 'error_handler' ERR
+
     unpigz -cdf $fasta | \\
     kalign \\
         $args \\

diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml
@@ -12,13 +12,13 @@ tools:
       tool_dev_url: "https://github.com/TimoLassmann/kalign"
       doi: "10.1093/bioinformatics/btz795"
       licence: ["GPL v3"]
-      identifier: ""
+      identifier: "biotools:kalign"
 input:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. `[ id:'test']`
+          e.g. [ id:'test']
     - fasta:
         type: file
         description: Input sequences in FASTA format. May be gzipped or uncompressed.

diff --git a/modules/nf-core/kalign/align/tests/main.nf.test.snap b/modules/nf-core/kalign/align/tests/main.nf.test.snap
@@ -11,7 +11,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
+                    "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
                 ],
                 "alignment": [
                     [
@@ -22,11 +22,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
+                    "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
                 ]
             }
         ],
-        "timestamp": "2024-03-22T16:42:01.934768"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-20T12:44:18.067352"
     },
     "SARS-CoV-2 scaffolds fasta - compressed": {
         "content": [
@@ -40,7 +44,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
+                    "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
                 ],
                 "alignment": [
                     [
@@ -51,10 +55,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe"
+                    "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94"
                 ]
             }
         ],
-        "timestamp": "2024-03-22T16:42:07.734293"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-09-20T12:44:31.031883"
     }
 }