From fd0aed8aa95e62ce823284a7cc89a61cdb551897 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 12:17:35 +0200
Subject: [PATCH 1/7] Display message when error 132 found

---
 modules/nf-core/kalign/align/main.nf | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf
index 5d575dc71ea..7262e246231 100644
--- a/modules/nf-core/kalign/align/main.nf
+++ b/modules/nf-core/kalign/align/main.nf
@@ -23,6 +23,16 @@ 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.\n\n"
+        else
+            trap - ERR
+            return \$exit_code
+        fi
+    }
+    
     unpigz -cdf $fasta | \\
     kalign \\
         $args \\

From a0d8e558c532e4e81aae23c2adbbf866904315aa Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 12:46:09 +0200
Subject: [PATCH 2/7] Update snapshots

---
 .../kalign/align/tests/main.nf.test.snap      | 20 +++++++++++++------
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/kalign/align/tests/main.nf.test.snap b/modules/nf-core/kalign/align/tests/main.nf.test.snap
index da6fc94c52e..cee655899ec 100644
--- 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"
     }
 }
\ No newline at end of file

From be7a7e891d0e8758888bfadc494ceba86bdf3cc9 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 12:46:19 +0200
Subject: [PATCH 3/7] Make lint happy

---
 modules/nf-core/kalign/align/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf
index 7262e246231..5cc23e2927b 100644
--- a/modules/nf-core/kalign/align/main.nf
+++ b/modules/nf-core/kalign/align/main.nf
@@ -26,13 +26,13 @@ process KALIGN_ALIGN {
     error_handler() {
     exit_code=\$?
         if [ \$exit_code -eq 132 ]; then
-            echo "\n\nKALIGN failed because is incompatible with some CPU types.\n\n"
+            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
     }
-    
+
     unpigz -cdf $fasta | \\
     kalign \\
         $args \\

From c38febf4fd44030fa7a549dc6226b46641c5b996 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 14:17:13 +0200
Subject: [PATCH 4/7] Add call to the function with trap

---
 modules/nf-core/kalign/align/main.nf | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf
index 5cc23e2927b..ca32dc4d5bf 100644
--- a/modules/nf-core/kalign/align/main.nf
+++ b/modules/nf-core/kalign/align/main.nf
@@ -32,6 +32,8 @@ process KALIGN_ALIGN {
             return \$exit_code
         fi
     }
+    
+    trap 'error_handler' ERR
 
     unpigz -cdf $fasta | \\
     kalign \\

From 0a4197ea1f81f4fd357e872a85b79e229ebb6935 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 14:53:11 +0200
Subject: [PATCH 5/7] Make nf-core lint happy

---
 modules/nf-core/kalign/align/meta.yml | 58 ++++++++++++++++-----------
 1 file changed, 34 insertions(+), 24 deletions(-)

diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml
index 187f6bc3fae..415ceee2fa0 100644
--- a/modules/nf-core/kalign/align/meta.yml
+++ b/modules/nf-core/kalign/align/meta.yml
@@ -12,36 +12,46 @@ tools:
       tool_dev_url: "https://github.com/TimoLassmann/kalign"
       doi: "10.1093/bioinformatics/btz795"
       licence: ["GPL v3"]
+      identifier: "biotools:kalign"
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test']`
-  - fasta:
-      type: file
-      description: Input sequences in FASTA format. May be gzipped or uncompressed.
-      pattern: "*.{fa,fasta}{.gz,}"
-  - compress:
-      type: boolean
-      description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          - - meta: 
+           type: map 
+           description: | 
+             Groovy Map containing sample information 
+             e.g. [ id:'test', single_end:false ] 
+    - fasta:
+        type: file
+        description: Input sequences in FASTA format. May be gzipped or uncompressed.
+        pattern: "*.{fa,fasta}{.gz,}"
+  - - compress:
+        type: boolean
+        description: Flag representing whether the output MSA should be compressed.
+          Set to true to enable/false to disable compression. Compression is done using
+          pigz, and is multithreaded.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'test']`
   - alignment:
-      type: file
-      description: Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`.
-      pattern: "*.{aln}{.gz,}"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test']`
+      - "*.aln{.gz,}":
+          type: file
+          description: Alignment file. May be gzipped or uncompressed, depending on if
+            `compress` is set to `true` or `false`.
+          pattern: "*.{aln}{.gz,}"
   - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@luisas"
   - "@JoseEspinosa"
 maintainers:
   - "@luisas"
-  - "@JoseEspinosa"
+  - "@JoseEspinosa"
\ No newline at end of file

From 95ba3ba5c27c22081c1c56386485d3d7c0e32387 Mon Sep 17 00:00:00 2001
From: JoseEspinosa <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 15:00:40 +0200
Subject: [PATCH 6/7] More linting

---
 modules/nf-core/kalign/align/main.nf  | 2 +-
 modules/nf-core/kalign/align/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf
index ca32dc4d5bf..59998df1adc 100644
--- a/modules/nf-core/kalign/align/main.nf
+++ b/modules/nf-core/kalign/align/main.nf
@@ -32,7 +32,7 @@ process KALIGN_ALIGN {
             return \$exit_code
         fi
     }
-    
+
     trap 'error_handler' ERR
 
     unpigz -cdf $fasta | \\
diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml
index f1061978ec4..44cd288e734 100644
--- a/modules/nf-core/kalign/align/meta.yml
+++ b/modules/nf-core/kalign/align/meta.yml
@@ -17,7 +17,7 @@ input:
   - - meta:
         type: map
         description: |
-          Groovy Map containing sample information 
+          Groovy Map containing sample information
           e.g. [ id:'test']
     - fasta:
         type: file

From bd7d9f5b7d6fe9171e2c784f74e313cef6881cd5 Mon Sep 17 00:00:00 2001
From: Jose Espinosa-Carrasco <kadomu@gmail.com>
Date: Fri, 20 Sep 2024 13:44:41 +0000
Subject: [PATCH 7/7] Make lint happy

---
 modules/nf-core/kalign/align/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml
index 44cd288e734..66c5ca8af95 100644
--- a/modules/nf-core/kalign/align/meta.yml
+++ b/modules/nf-core/kalign/align/meta.yml
@@ -50,4 +50,4 @@ authors:
   - "@JoseEspinosa"
 maintainers:
   - "@luisas"
-  - "@JoseEspinosa"
\ No newline at end of file
+  - "@JoseEspinosa"