add tests for ena_webin_cli

modules/local/ena_webin_cli/main.nf

@@ -53,6 +53,10 @@ process ENA_WEBIN_CLI {
         # there was attempt to re-submit already submitted genome
         export STATUS="success"
         true
+    elif grep -q "Submission(s) validated successfully" "${prefix}_webin-cli.report"; then
+        # we ran with -validate flag
+        export STATUS="success"
+        true
     else
         export STATUS="failed"
         false

modules/local/ena_webin_cli/main.nf.test

@@ -0,0 +1,86 @@
+nextflow_process {
+
+    name "Test Process ENA_WEBIN_CLI"
+    script "modules/local/ena_webin_cli/main.nf"
+    process "ENA_WEBIN_CLI"
+
+    test("Run validate with no failures") {
+
+        when {
+            params {
+                webincli_submit = false
+            }
+            process {
+                """
+                input[0] = Channel.of(
+                    tuple(
+                        [id: 'lachnospira_eligens'],
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true),
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true)
+                    )
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                assert process.success
+                assert process.out.upload_status[0][1] == 'success'
+                assert path(process.out.webin_report[0][1]).readLines()[0].contains("Submission(s) validated successfully")
+                assert snapshot(process.out.versions).match()
+            }
+        }
+
+    }
+
+    test("Run push with no failures") {
+        setup {
+            run("GENERATE_TEST_DATA") {
+                script "./setup_test.nf"
+                process {
+                    """
+                    input[0] = Channel.of(
+                        file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/lachnospira_eligens.manifest", checkIfExists: true)
+                    )
+                    """
+                }
+            }
+
+        }
+
+        when {
+            params {
+                webincli_submit = true
+                test_upload = true
+            }
+            process {
+                """
+                def fasta = file("https://github.com/nf-core/test-datasets/raw/refs/heads/seqsubmit/test_data/bins/bin_lachnospira_eligens.fa.gz", checkIfExists: true)
+
+                input[0] = GENERATE_TEST_DATA.out.test_manifest.map { manifest ->
+                    tuple(
+                        [id: 'lachnospira_eligens'],
+                        fasta,
+                        file(manifest)
+                    )
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll {
+                assert process.success
+                assert process.out.upload_status[0][1] == 'success'
+                assert snapshot(process.out.versions).match()
+                assert path(process.out.webin_report[0][1]).readLines()[1].contains("Submission(s) validated successfully")
+                assert path(process.out.webin_report[0][1]).readLines()[5].contains("The submission has been completed successfully")
+                assert path(process.out.webin_report[0][1]).readLines()[6].contains("This was a TEST submission(s)")
+
+            }
+        }
+
+    }
+
+}

modules/local/ena_webin_cli/main.nf.test.snap

@@ -0,0 +1,26 @@
+{
+    "Run validate with no failures": {
+        "content": [
+            [
+                "versions.yml:md5,a38fb03bead632d71062a101d7889ded"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T14:09:00.202532371"
+    },
+    "Run push with no failures": {
+        "content": [
+            [
+                "versions.yml:md5,a38fb03bead632d71062a101d7889ded"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-29T14:01:42.491885321"
+    }
+}

modules/local/ena_webin_cli/setup_test.nf

@@ -0,0 +1,17 @@
+process GENERATE_TEST_DATA {
+    label 'process_low'
+    container "quay.io/biocontainers/ena-webin-cli:9.0.1--hdfd78af_1"
+
+    input:
+    path(manifest_template)
+
+    output:
+    path("*.manifest"), emit: test_manifest
+
+    script:
+    """
+    timestamp="\$(date +%s)"
+
+    sed -E "s/^(ASSEMBLYNAME\t[^\t]+)/\\1_\${timestamp}/" "${manifest_template}" > "lachnospira_eligens_dynamic_fixture.manifest"
+    """
+}