Add stub blocks to all local modules

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #325](https://github.com/nf-core/fetchngs/pull/325) - Add wget wait time for retries
 - [PR #333](https://github.com/nf-core/fetchngs/pull/333) - Add logo
 - [PR #365](https://github.com/nf-core/fetchngs/pull/365) - Template update for nf-core/tools v3.5.2, including topic channels for version reporting
+- [PR #368](https://github.com/nf-core/fetchngs/pull/XXX) - Add stub blocks to all local modules
 
 ### Software dependencies
 

modules/local/aspera_cli/main.nf

@@ -55,4 +55,20 @@ process ASPERA_CLI {
         md5sum -c ${meta.id}_2.fastq.gz.md5
         """
     }
+
+    stub:
+    if (meta.single_end) {
+        """
+        echo | gzip > ${meta.id}.fastq.gz
+        touch ${meta.id}.fastq.gz.md5
+        """
+    } else {
+        """
+        echo | gzip > ${meta.id}_1.fastq.gz
+        echo | gzip > ${meta.id}_2.fastq.gz
+        touch ${meta.id}_1.fastq.gz.md5
+        touch ${meta.id}_2.fastq.gz.md5
+        """
+    }
+
 }

modules/local/aspera_cli/tests/main.nf.test

@@ -28,4 +28,29 @@ nextflow_process {
             )
         }
     }
-}
+
+    test("Should run without failures - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    [
+                        'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz',
+                        'fasp.sra.ebi.ac.uk:/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz'
+                    ]
+                ]
+                input[1] = 'era-fasp'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+}

modules/local/multiqc_mappings_config/main.nf

@@ -19,4 +19,9 @@ process MULTIQC_MAPPINGS_CONFIG {
         $csv \\
         multiqc_config.yml
     """
+
+    stub:
+    """
+    touch multiqc_config.yml
+    """
 }

modules/local/multiqc_mappings_config/tests/main.nf.test

@@ -21,4 +21,22 @@ nextflow_process {
             )
         }
     }
+
+    test("Should run without failures - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = file(params.pipelines_testdata_base_path + 'csv/SRX9626017_SRR13191702.mappings.csv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
 }

modules/local/multiqc_mappings_config/tests/main.nf.test.snap

@@ -24,7 +24,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-13T15:41:59.602846",
+        "timestamp": "2026-05-06T16:00:30.170721088",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

modules/local/sra_fastq_ftp/main.nf

@@ -48,4 +48,19 @@ process SRA_FASTQ_FTP {
         md5sum -c ${meta.id}_2.fastq.gz.md5
 """
     }
+
+    stub:
+    if (meta.single_end) {
+        """
+        echo | gzip > ${meta.id}.fastq.gz
+        touch ${meta.id}.fastq.gz.md5
+        """
+    } else {
+        """
+        echo | gzip > ${meta.id}_1.fastq.gz
+        echo | gzip > ${meta.id}_2.fastq.gz
+        touch ${meta.id}_1.fastq.gz.md5
+        touch ${meta.id}_2.fastq.gz.md5
+        """
+    }
 }

modules/local/sra_fastq_ftp/tests/main.nf.test

@@ -27,4 +27,28 @@ nextflow_process {
             )
         }
     }
+
+    test("Should run without failures - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'SRX9626017_SRR13191702', single_end:false, md5_1: '89c5be920021a035084d8aeb74f32df7', md5_2: '56271be38a80db78ef3bdfc5d9909b98' ], // meta map
+                    [
+                        'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_1.fastq.gz',
+                        'ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/SRR13191702_2.fastq.gz'
+                    ]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
 }

modules/local/sra_fastq_ftp/tests/main.nf.test.snap

@@ -74,7 +74,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-13T15:42:09.490402",
+        "timestamp": "2026-05-06T16:01:04.565094912",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

modules/local/sra_ids_to_runinfo/main.nf

@@ -25,4 +25,9 @@ process SRA_IDS_TO_RUNINFO {
         ${id}.runinfo.tsv \\
         $metadata_fields
     """
+
+    stub:
+    """
+    touch ${id}.runinfo.tsv
+    """
 }

modules/local/sra_ids_to_runinfo/tests/main.nf.test

@@ -22,4 +22,23 @@ nextflow_process {
             )
         }
     }
+
+    test("Should run without failures - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = 'SRR13191702'
+                input[1] = ''
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
 }

modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap

@@ -24,7 +24,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-13T15:42:19.072989",
+        "timestamp": "2026-05-06T16:01:36.028872084",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

modules/local/sra_runinfo_to_ftp/main.nf

@@ -19,4 +19,9 @@ process SRA_RUNINFO_TO_FTP {
         ${runinfo.join(',')} \\
         ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
     """
+
+    stub:
+    """
+    touch ${runinfo.toString().tokenize(".")[0]}.runinfo_ftp.tsv
+    """
 }

modules/local/sra_runinfo_to_ftp/tests/main.nf.test

@@ -21,4 +21,22 @@ nextflow_process {
             )
         }
     }
+
+    test("Should run without failures - stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = file(params.pipelines_testdata_base_path + 'tsv/SRR13191702.runinfo.tsv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
 }

modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap

@@ -24,7 +24,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-13T15:42:31.518986",
+        "timestamp": "2026-05-06T16:02:10.236064039",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "25.10.4"

modules/local/sra_to_samplesheet/tests/main.nf.test

@@ -24,4 +24,5 @@ nextflow_process {
             )
         }
     }
+
 }

modules/local/sra_to_samplesheet/tests/main.nf.test.snap

@@ -108,10 +108,10 @@
                 ]
             }
         ],
+        "timestamp": "2024-02-28T11:51:38.244046",
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-02-28T11:51:38.244046"
+        }
     }
 }

workflows/fetchngs.nf

@@ -60,6 +60,7 @@ workflow FETCHNGS {
     SRA_RUNINFO_TO_FTP
         .out
         .tsv
+        .filter { it.size() > 0 }
         .splitCsv(header:true, sep:'\t')
         .map {
             meta ->