addedd optional output channel for lib files (nf-core#5257)

* addedd optional output channel for lib files

* added the output description for lin in meta.yml

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:

modules/nf-core/tcoffee/align/meta.yml

@@ -61,14 +61,20 @@ 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
       pattern: "versions.yml"
 authors:
   - "@luisas"
   - "@JoseEspinosa"
+  - "@alessiovignoli"
 maintainers:
   - "@luisas"
   - "@JoseEspinosa"
   - "@lrauschning"
+  - "@alessiovignoli"

modules/nf-core/tcoffee/align/tests/lib.config

@@ -0,0 +1,3 @@
+process {
+    ext.args = { "-output fasta_aln -out_lib=sample_lib1.tc_lib" }
+}

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") }
+            )
+        }
+    }
 }