Patch-functional-annotations

subworkflows/local/functional_annotation/meta.yml

@@ -0,0 +1,63 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
+name: "FUNCTIIONAL_ANNOTATIONS"
+description: Perform local functional annotation on protien sequences
+keywords:
+  - fasta
+  - sequences
+  - functional
+  - domain
+  - annotation
+  - database
+  - download
+  - HMM
+components:
+  - aria2
+  - hmmer/hmmsearch
+input:
+  - ch_fasta:
+      type: file
+      description: |
+        Amino acid fasta file containing amino acid sequences for annotation
+        Structure: [ val(meta), [ path(fasta) ] ]
+  - skip_pfam:
+      type: boolean
+      description: |
+        Skip domain annotation with Pfam
+  - pfam_db:
+      type: string
+      description: |
+        Path to an existing HMM Pfam library on the system. If provided, the ARIA2_PFAM db download will be skipped.
+  - pfam_latest_link:
+      type: string
+      description: |
+        Path to the latest Pfam HMM database, to download
+  - skip_funfam:
+      type: boolean
+      description: |
+        Skip domain annotation with FunFam
+  - funfam_db:
+      type: string
+      description: |
+        Path to an existing HMM FunFam library on the system. If provided, the ARIA2_FUNFAM db download will be skipped.
+  - funfam_latest_link:
+      type: string
+      description: |
+        Path to the latest FunFam HMM database, to download
+output:
+  - pfam_domains:
+      type: file
+      description: |
+        domtbl.gz files with pfam domain annotation for input amino acid sequences
+  - funfam_domains:
+      type: file
+      description: |
+        domtbl.gz files with funfam domain annotation for input amino acid sequences
+  - versions:
+      type: file
+      description: |
+        Versions file containing the software versions used in the workflow
+authors:
+  - "@vagkaratzas"
+  - "@Muskan-2464"
+maintainers:
+  - "@vagkaratzas"

tests/nf test

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+nextflow_workflow {
+
+    name "Test Subworkflow functional_annotation"
+    script "../main.nf"
+    workflow "FUNCTIIONAL_ANNOTATIONS"
+
+    test("Should run functional annotation successfully") {
+
+        when {
+            workflow {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                input[1] = false // skip_pfam
+                input[2] = []    // pfam_db
+                input[3] = "https://raw.githubusercontent.com/nf-core/test-datasets/multiqc/testdata/set_indices.txt"
+                input[4] = true  // skip_funfam
+                input[5] = []    // funfam_db
+                input[6] = []    // funfam_latest_link
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}