Update AMPCOMBI_PARSETABLES to Include extra output channel (#11989)

* Include extra output channel

* Switch database due to dead link for DRAMP

* Fix variable tests

* Fix lintign

Author: jfy133

modules/nf-core/ampcombi2/parsetables/main.nf

@@ -3,9 +3,9 @@ process AMPCOMBI2_PARSETABLES {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:3.0.0--pyhdfd78af_0':
-        'quay.io/biocontainers/ampcombi:3.0.0--pyhdfd78af_0' }"
+    container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
+        ? 'https://depot.galaxyproject.org/singularity/ampcombi:3.0.0--pyhdfd78af_0'
+        : 'quay.io/biocontainers/ampcombi:3.0.0--pyhdfd78af_0'}"
 
     input:
     tuple val(meta), path(amp_input)
@@ -16,18 +16,19 @@ process AMPCOMBI2_PARSETABLES {
     path opt_interproscan
 
     output:
-    tuple val(meta), path("${prefix}/")                            , emit: sample_dir
-    tuple val(meta), path("Ampcombi_parse_tables.log")             , emit: full_log   , optional:true
-    tuple val(meta), path("amp_${opt_amp_db}_database/")           , emit: db         , optional:true
+    tuple val(meta), path("${prefix}/"), emit: sample_dir
+    tuple val(meta), path("${prefix}/${prefix}_ampcombi.tsv"), emit: tsv, optional: true
+    tuple val(meta), path("Ampcombi_parse_tables.log"), emit: full_log, optional: true
+    tuple val(meta), path("amp_${opt_amp_db}_database/"), emit: db, optional: true
     tuple val("${task.process}"), val('ampcombi'), eval("ampcombi --version | sed 's/ampcombi //'"), emit: versions_ampcombi, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args   = task.ext.args   ?: ''
-    prefix     = task.ext.prefix ?: "${meta.id}"
-    def db_dir = opt_amp_db_dir  ? "--amp_database_dir ${opt_amp_db_dir}" : ""
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
     def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
 
     """

modules/nf-core/ampcombi2/parsetables/meta.yml

@@ -87,6 +87,19 @@ output:
           description: The output directory that contains the summary output and related
             alignment files for one sample.
           pattern: "/*"
+  tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ${prefix}/${prefix}_ampcombi.tsv:
+          type: file
+          description: A TSV file containing the summary of the AMP detection results for
+            one sample.
+          pattern: "/*_ampcombi.tsv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
   full_log:
     - - meta:
           type: map

modules/nf-core/ampcombi2/parsetables/tests/main.nf.test

@@ -28,7 +28,7 @@ nextflow_process {
                 input[0] = amp_input
                 input[1] = faa_input
                 input[2] = gbk_input
-                input[3] = 'DRAMP'
+                input[3] = 'APD'
                 input[4] = []
                 input[5] = []
                 """
@@ -38,10 +38,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.sample_dir.collect { file(it[1]).getName() } +
-                                    process.out.full_log.collect { file(it[1]).readLines().contains("File downloaded successfully") } +
-                                    process.out.db.collect { file(it[1]).getName() } +
-                                    process.out.findAll { key, val -> key.startsWith('versions') } ).match() }
+                { assert snapshot(
+                    process.out.sample_dir.collect { file(it[1]).getName() },
+                    path(process.out.tsv[0][1]).getText().contains("sample_1"),
+                    path(process.out.full_log[0][1]).getText().contains("Creating MMseqs2 directory for fasta file in"),
+                    process.out.db.collect { file(it[1]).getName() },
+                    process.out.findAll { key, val -> key.startsWith('versions') } ).match() },
             )
         }
     }
@@ -63,7 +65,7 @@ nextflow_process {
                 input[0] = amp_input
                 input[1] = faa_input
                 input[2] = gbk_input
-                input[3] = 'DRAMP'
+                input[3] = 'APD'
                 input[4] = []
                 input[5] = []
                 """

modules/nf-core/ampcombi2/parsetables/tests/main.nf.test.snap

@@ -2,24 +2,27 @@
     "ampcombi2_parsetables - metagenome": {
         "content": [
             [
-                "sample_1",
-                false,
-                "amp_DRAMP_database",
-                {
-                    "versions_ampcombi": [
-                        [
-                            "AMPCOMBI2_PARSETABLES",
-                            "ampcombi",
-                            "3.0.0"
-                        ]
+                "sample_1"
+            ],
+            true,
+            true,
+            [
+                "amp_APD_database"
+            ],
+            {
+                "versions_ampcombi": [
+                    [
+                        "AMPCOMBI2_PARSETABLES",
+                        "ampcombi",
+                        "3.0.0"
                     ]
-                }
-            ]
+                ]
+            }
         ],
-        "timestamp": "2026-04-23T19:09:35.917379447",
+        "timestamp": "2026-06-12T15:33:40.134609032",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     },
     "ampcombi2_parsetables - metagenome - stub": {
@@ -43,10 +46,18 @@
                         {
                             "id": "sample_1"
                         },
-                        "Ampcombi_parse_tables.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample_1_ampcombi.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
+                    [
+                        {
+                            "id": "sample_1"
+                        },
+                        "Ampcombi_parse_tables.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
                     [
                         {
                             "id": "sample_1"
@@ -67,7 +78,7 @@
                         ]
                     ]
                 ],
-                "3": [
+                "4": [
                     [
                         "AMPCOMBI2_PARSETABLES",
                         "ampcombi",
@@ -116,6 +127,14 @@
                         ]
                     ]
                 ],
+                "tsv": [
+                    [
+                        {
+                            "id": "sample_1"
+                        },
+                        "sample_1_ampcombi.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions_ampcombi": [
                     [
                         "AMPCOMBI2_PARSETABLES",
@@ -125,10 +144,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-23T19:17:18.712188072",
+        "timestamp": "2026-06-12T14:49:48.909595472",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     }
 }