nf-core · maxulysse · Aug 20, 2026 · Aug 20, 2026 · Aug 20, 2026 · Aug 20, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#280](https://github.com/nf-core/seqinspector/pull/280) Add validation for missing `--bait_intervals` and `--target_intervals` when `picard_collecthsmetrics` is requested (@maxulysse)
+- [#280](https://github.com/nf-core/seqinspector/pull/280) Add validation for missing fasta when picard or riker is requested (@maxulysse)
+- [#280](https://github.com/nf-core/seqinspector/pull/280) Add validation for unsupported riker collectors (wgs, gcbias, error, rna) that require interval files not yet supported as pipeline parameters (@maxulysse)
+
 ### `Fixed`
 
 ### `Changed`

diff --git a/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf b/subworkflows/local/utils_nfcore_seqinspector_pipeline/main.nf
@@ -166,9 +166,14 @@ ${subsampled_info}-\033[2m----------------------------------------------------\0
             }
         }
 
+    // Picard and riker require a reference FASTA for alignment and metrics
     if (!(fasta) && (("picard_collecthsmetrics" in tools) || ("picard_collectmultiplemetrics" in tools) || ("riker" in tools))) {
-        log.warn("No fasta was provided, but picard or riker was requested")
-        log.warn("BWAMEM2, SAMTOOLS, PICARD and RIKER processes will be skipped")
+        error("No fasta was provided, but picard or riker was requested. A reference FASTA is required for these tools.")
+    }
+
+    // CollectHsMetrics requires bait and target interval lists
+    if ('picard_collecthsmetrics' in tools && (!params.bait_intervals || !params.target_intervals)) {
+        error("picard_collecthsmetrics was requested but --bait_intervals and --target_intervals were not provided. Both are required for CollectHsMetrics.")
     }
 
     if ('toulligqc' in tools && 'emulate_amd64' in workflow.profile.tokenize(",")) {
@@ -238,6 +243,7 @@ workflow PIPELINE_COMPLETION {
 def validateInputParameters(tools, riker_args) {
     genomeExistsError()
     rikerHybcapError(tools, riker_args)
+    rikerUnsupportedCollectorsError(tools, riker_args)
 }
 
 //
@@ -274,6 +280,23 @@ def rikerHybcapError(tools, riker_args) {
     }
 }
 
+//
+// Exit pipeline if riker collectors requiring interval files are requested
+// but the pipeline does not yet support providing those files
+//
+def rikerUnsupportedCollectorsError(tools, riker_args) {
+    if ('riker' in tools && riker_args) {
+        def unsupported = []
+        if (riker_args.contains('wgs'))       unsupported << 'wgs (requires --wgs_intervals)'
+        if (riker_args.contains('gcbias'))    unsupported << 'gcbias (requires --gcbias_exclude_intervals)'
+        if (riker_args.contains('error'))     unsupported << 'error (requires --error_vcf and/or --error_intervals)'
+        if (riker_args.contains('rna'))       unsupported << 'rna (requires --rna_gene_model and/or --rna_ribosomal_intervals)'
+        if (unsupported) {
+            error("riker_args contains collectors that require interval files not yet supported as pipeline parameters: ${unsupported.join(', ')}.")
+        }
+    }
+}
+
 //
 // Generate methods description for MultiQC
 //

diff --git a/tests/no_genome.nf.test b/tests/no_genome.nf.test
@@ -11,7 +11,7 @@ nextflow_pipeline {
             params: [
                 input: pipelines_testdata_base_path + 'seqinspector/samplesheet/1.0/miseq.csv',
                 genome: null,
-                tools: 'fastqscreen,picard_collecthsmetrics',
+                tools: 'fastqscreen',
                 tools_bundle: null,
             ],
         ],
@@ -20,7 +20,7 @@ nextflow_pipeline {
             params: [
                 input: pipelines_testdata_base_path + 'seqinspector/samplesheet/1.0/miseq.csv',
                 genome: null,
-                tools: 'fastqscreen,picard_collecthsmetrics',
+                tools: 'fastqscreen',
                 tools_bundle: null,
             ],
             stub: true,

diff --git a/tests/no_genome.nf.test.snap b/tests/no_genome.nf.test.snap
@@ -1,4 +1,22 @@
 {
+    "MiSeq data test - no genome with picard - should fail": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            "No stable content",
+            "No BAM files",
+            "No warnings",
+            [
+                "[ERROR] No fasta was provided, but picard or riker was requested. A reference FASTA is required for these tools."
+            ]
+        ],
+        "timestamp": "2026-08-20T13:38:47.440297992",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
     "MiSeq data test - no genome": {
         "content": [
             6,
@@ -189,5 +207,23 @@
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"
         }
+    },
+    "MiSeq data test - no genome with picard - stub": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            [
+                "[WARN] WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, [CONTAINER]`."
+            ],
+            [
+                "[ERROR] No fasta was provided, but picard or riker was requested. A reference FASTA is required for these tools."
+            ]
+        ],
+        "timestamp": "2026-08-20T13:39:11.195831371",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
diff --git a/tests/tools_picard.nf.test b/tests/tools_picard.nf.test
@@ -26,6 +26,50 @@ nextflow_pipeline {
             ],
             stub: true,
         ],
+        [
+            name: "NovaSeq6000 data test - picard_collecthsmetrics missing intervals - should fail",
+            params: [
+                tools: 'picard_collecthsmetrics',
+                tools_bundle: null,
+            ],
+            failure: true,
+            snapshot_include: 'bait_intervals',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - picard_collecthsmetrics missing intervals - stub",
+            params: [
+                tools: 'picard_collecthsmetrics',
+                tools_bundle: null,
+            ],
+            failure: true,
+            stub: true,
+            snapshot_include: 'bait_intervals',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - picard missing fasta - should fail",
+            params: [
+                tools: 'picard_collecthsmetrics,picard_collectmultiplemetrics',
+                tools_bundle: null,
+                genome: null,
+            ],
+            failure: true,
+            snapshot_include: 'fasta',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - picard missing fasta - stub",
+            params: [
+                tools: 'picard_collecthsmetrics,picard_collectmultiplemetrics',
+                tools_bundle: null,
+                genome: null,
+            ],
+            failure: true,
+            stub: true,
+            snapshot_include: 'fasta',
+            snapshot: 'stdout,stderr',
+        ],
     ]
 
     // Generate tests for each scenario

diff --git a/tests/tools_picard.nf.test.snap b/tests/tools_picard.nf.test.snap
@@ -1,4 +1,40 @@
 {
+    "NovaSeq6000 data test - picard missing fasta - stub": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            [
+                "[WARN] WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, [CONTAINER]`."
+            ],
+            [
+                "[ERROR] No fasta was provided, but picard or riker was requested. A reference FASTA is required for these tools."
+            ]
+        ],
+        "timestamp": "2026-08-20T13:42:47.524968852",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "NovaSeq6000 data test - picard_collecthsmetrics missing intervals - should fail": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            "No stable content",
+            "No BAM files",
+            "No warnings",
+            [
+                "[ERROR] picard_collecthsmetrics was requested but --bait_intervals and --target_intervals were not provided. Both are required for CollectHsMetrics."
+            ]
+        ],
+        "timestamp": "2026-08-20T11:25:23.275081727",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
     "NovaSeq6000 data test - picard_collecthsmetrics and picard_collectmultiplemetrics": {
         "content": [
             28,
@@ -693,5 +729,41 @@
             "nf-test": "0.9.5",
             "nextflow": "26.04.4"
         }
+    },
+    "NovaSeq6000 data test - picard missing fasta - should fail": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            "No stable content",
+            "No BAM files",
+            "No warnings",
+            [
+                "[ERROR] No fasta was provided, but picard or riker was requested. A reference FASTA is required for these tools."
+            ]
+        ],
+        "timestamp": "2026-08-20T13:42:28.564703052",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
+    },
+    "NovaSeq6000 data test - picard_collecthsmetrics missing intervals - stub": {
+        "content": [
+            [
+                "pipeline_info"
+            ],
+            [
+                "[WARN] WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected. HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, [CONTAINER]`."
+            ],
+            [
+                "[ERROR] picard_collecthsmetrics was requested but --bait_intervals and --target_intervals were not provided. Both are required for CollectHsMetrics."
+            ]
+        ],
+        "timestamp": "2026-08-20T11:25:48.76823048",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
diff --git a/tests/tools_riker.nf.test b/tests/tools_riker.nf.test
@@ -54,6 +54,50 @@ nextflow_pipeline {
             snapshot_include: 'hybcap',
             snapshot: 'stdout,stderr',
         ],
+        [
+            name: "NovaSeq6000 data test - riker with wgs collector - should fail",
+            params: [
+                tools: 'riker',
+                tools_bundle: null,
+                riker_args: '--tools wgs',
+            ],
+            failure: true,
+            snapshot_include: 'wgs',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - riker with gcbias collector - should fail",
+            params: [
+                tools: 'riker',
+                tools_bundle: null,
+                riker_args: '--tools gcbias',
+            ],
+            failure: true,
+            snapshot_include: 'gcbias',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - riker with error collector - should fail",
+            params: [
+                tools: 'riker',
+                tools_bundle: null,
+                riker_args: '--tools error',
+            ],
+            failure: true,
+            snapshot_include: 'error',
+            snapshot: 'stdout,stderr',
+        ],
+        [
+            name: "NovaSeq6000 data test - riker with rna collector - should fail",
+            params: [
+                tools: 'riker',
+                tools_bundle: null,
+                riker_args: '--tools rna',
+            ],
+            failure: true,
+            snapshot_include: 'rna',
+            snapshot: 'stdout,stderr',
+        ],
     ]
 
     // Generate tests for each scenario