From b7689e6b3c9003b58f7853bae896a727a5e7d44e Mon Sep 17 00:00:00 2001
From: alessiovignoli <45239231+alessiovignoli@users.noreply.github.com>
Date: Tue, 19 Mar 2024 15:35:03 +0100
Subject: [PATCH] addedd optional output channel for lib files (#5257)

* addedd optional output channel for lib files

* added the output description for lin in meta.yml
---
 modules/nf-core/tcoffee/align/main.nf         |  2 ++
 modules/nf-core/tcoffee/align/meta.yml        |  6 ++++
 .../nf-core/tcoffee/align/tests/lib.config    |  3 ++
 .../nf-core/tcoffee/align/tests/main.nf.test  | 27 +++++++++++++++++
 .../tcoffee/align/tests/main.nf.test.snap     | 29 +++++++++++++++++++
 5 files changed, 67 insertions(+)
 create mode 100644 modules/nf-core/tcoffee/align/tests/lib.config

diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf
index 671aca8eacc9..e159bb801e23 100644
--- a/modules/nf-core/tcoffee/align/main.nf
+++ b/modules/nf-core/tcoffee/align/main.nf
@@ -15,6 +15,8 @@ process TCOFFEE_ALIGN {
 
     output:
     tuple val(meta), path("*.aln{.gz,}"), emit: alignment
+    // in the args there might be the request to generate a lib file, so the following is an optional output
+    tuple val(meta), path("*.*lib")      , emit: lib, optional : true
     path "versions.yml"                 , emit: versions
 
     when:
diff --git a/modules/nf-core/tcoffee/align/meta.yml b/modules/nf-core/tcoffee/align/meta.yml
index 6cfcc72d46aa..4125d1ed2c24 100644
--- a/modules/nf-core/tcoffee/align/meta.yml
+++ b/modules/nf-core/tcoffee/align/meta.yml
@@ -61,6 +61,10 @@ output:
       type: file
       description: Alignment file in FASTA format. May be gzipped.
       pattern: "*.aln{.gz,}"
+  - lib:
+      type: file
+      description: optional output, the library generated from the MSA file.
+      pattern: "*.*lib"
   - versions:
       type: file
       description: File containing software versions
@@ -68,7 +72,9 @@ output:
 authors:
   - "@luisas"
   - "@JoseEspinosa"
+  - "@alessiovignoli"
 maintainers:
   - "@luisas"
   - "@JoseEspinosa"
   - "@lrauschning"
+  - "@alessiovignoli"
diff --git a/modules/nf-core/tcoffee/align/tests/lib.config b/modules/nf-core/tcoffee/align/tests/lib.config
new file mode 100644
index 000000000000..2fc113efa0e2
--- /dev/null
+++ b/modules/nf-core/tcoffee/align/tests/lib.config
@@ -0,0 +1,3 @@
+process {
+    ext.args = { "-output fasta_aln -out_lib=sample_lib1.tc_lib" }
+}
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test
index 9d66f86bf393..307534fb55cb 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test
@@ -147,4 +147,31 @@ nextflow_process {
         }
 
     }
+
+    test("fasta - align_with_lib") {
+
+        config "./lib.config"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:'test' ],
+                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                           ]
+                input[1] = [[:],[]]
+                input[2] = [[:],[],[]]
+                input[3] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.alignment).match("alignment - lib") },
+                { assert path(process.out.lib.get(0).get(1)).getText().contains("1ahl") },
+                { assert snapshot(process.out.versions).match("versions_lib") }
+            )
+        }
+    }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
index 9bdadbd4e429..dfef40a73527 100644
--- a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
+++ b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap
@@ -11,6 +11,18 @@
         },
         "timestamp": "2024-02-28T19:00:28.712838"
     },
+    "versions_lib": {
+        "content": [
+            [
+                "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T14:04:06.031557"
+    },
     "alignment - uncompressed": {
         "content": [
             [
@@ -52,6 +64,23 @@
         },
         "timestamp": "2024-02-28T19:00:10.618213"
     },
+    "alignment - lib": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T13:57:39.653762"
+    },
     "alignment": {
         "content": [
             [