Fix the input types to use a flat fasta and not an array

Author: olgabot

subworkflows/local/functional_annotation/main.nf

@@ -16,12 +16,11 @@ workflow FUNCTIONAL_ANNOTATION {
         .map {
             meta, fasta ->
             [
-                [id:"${meta.id}_${fasta[0].splitFasta(record: [id: true]).id[0].replaceAll(/\|/, '-')}"] ,
-                fasta[0].splitFasta(file:true)
+                [id:"${meta.id}_${fasta.splitFasta(record: [id: true]).id[0].replaceAll(/\|/, '-')}"] ,
+                fasta.splitFasta(file:true)
             ]
         }
         .transpose()
-        .view()
         .set { ch_multifasta }
 
     //

subworkflows/local/functional_annotation/tests/main.nf.test

@@ -16,7 +16,7 @@ nextflow_workflow {
 
 
     // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("snap25 isoforms - bcl2 - ced9") {
+    test("Test two input channels, one fasta record each") {
 
         when {
             params {
@@ -25,10 +25,45 @@ nextflow_workflow {
             workflow {
                 """
                 // TODO nf-core: define inputs of the workflow here. Example:
-                input[0] = Channel.of([
-                        [ id:'test', single_end:false ], // meta map
+                input[0] = Channel.fromList([
+                    [
+                        [ id:'T1024' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'proteinfold/testdata/sequences/T1024.fasta', checkIfExists: true)
+                    ],
+                    [
+                        [ id:'T1026' ], // meta map
+                        file(params.pipelines_testdata_base_path + 'proteinfold/testdata/sequences/T1026.fasta', checkIfExists: true)
+                    ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                // { assert snapshot(workflow.out).match()},
+                { assert workflow.success},
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+    }
+
+            // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("Test single input fasta with 4 fasta records: snap25 isoforms - bcl2 - ced9") {
+
+        when {
+            params {
+                pipelines_testdata_base_path = "https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/"
+            }
+            workflow {
+                """
+                // TODO nf-core: define inputs of the workflow here. Example:
+                input[0] = Channel.fromList([
+                    [
+                        [ id:'test' ], // meta map
                         file(params.pipelines_testdata_base_path + 'proteinannotator/reference/snap25_isoforms_bcl2_ced9.fasta', checkIfExists: true)
-                    ])
+                    ]
+                ])
                 """
             }
         }

subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf

@@ -71,16 +71,11 @@ workflow PIPELINE_INITIALISATION {
         .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
         .map {
             meta, fasta ->
-                return [ meta, [ fasta ] ]
+                return [ meta, fasta ]
         }
-        .groupTuple()
         .map { samplesheet ->
             validateInputSamplesheet(samplesheet)
         }
-        .map {
-            meta, fastas ->
-                return [ meta, fastas.flatten() ]
-        }
         .set { ch_samplesheet }
 
     emit: