Restructuring how symlinks work to avoid conflicts with file permissions

modules/nf-core/parabricks/fq2bam/main.nf

@@ -2,8 +2,6 @@ process PARABRICKS_FQ2BAM {
     tag "${meta.id}"
     label 'process_high'
     label 'process_gpu'
-    // needed by the module to run on a cluster because we need to copy the fasta reference, see https://github.com/nf-core/modules/issues/9230
-    stageInMode 'copy'
 
     container "nvcr.io/nvidia/clara/clara-parabricks:4.6.0-1"
 
@@ -44,14 +42,38 @@ process PARABRICKS_FQ2BAM {
     def known_sites_output_cmd = known_sites   ? "--out-recal-file ${prefix}.table" : ""
     def interval_file_command  = interval_file ? (interval_file instanceof List ? interval_file.collect { "--interval-file ${it}" }.join(' ') : "--interval-file ${interval_file}") : ""
 
-    def num_gpus   = task.accelerator ? "--num-gpus ${task.accelerator.request}" : ''
-    """
+    def num_gpus = task.accelerator ? "--num-gpus ${task.accelerator.request}" : ''
+
+    if (!fasta && extension=="cram") error "Fasta reference is required for CRAM output"
+
+    """    
+    # The section below checks if the reference is present with the index files. 
+    # If it is not, then we create a dummy reference file to allow Parabricks to run without erroring out 
+    # For BAMs, this index file is empty, for CRAMs we symlink the fasta to the expected index path 
+
     INDEX=`find -L ./ -name "*.amb" | sed 's/\\.amb\$//'`
-    cp ${fasta} \$INDEX
+
+    echo "Inferred reference at: \$INDEX"
+
+    dummy_index=0 
+    ref_path=${fasta}
+
+    if [[ "${extension}" == "bam" ]] && [ ! -e \$INDEX ]; then
+        echo "BAM requested but ref path does not exist. Creating dummy reference."
+        dummy_index=1
+        touch \$INDEX
+        ref_path="\$INDEX"
+    elif [[ "${extension}" == "cram" ]] && [ ! -e \$INDEX ]; then
+        echo "CRAM requested but ref does not follow pattern. Creating symlink."
+        dummy_index=1
+        ln -sf \$(realpath ${fasta}) \$(realpath \$INDEX)
+        ref_path="\$INDEX"
+    fi
 
     pbrun \\
         fq2bam \\
-        --ref \$INDEX \\
+        --preserve-file-symlinks \\
+        --ref \$ref_path \\
         ${in_fq_command} \\
         --out-bam ${prefix}.${extension} \\
         ${known_sites_command} \\
@@ -62,6 +84,11 @@ process PARABRICKS_FQ2BAM {
         --monitor-usage \\
         ${args}
 
+    # Remove the dummy index if we added one 
+    if [ dummy_index ]; then 
+        rm \$INDEX
+    fi
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
             pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )

modules/nf-core/parabricks/fq2bam/meta.yml

@@ -33,7 +33,7 @@ input:
           Groovy Map containing fasta information
     - fasta:
         type: file
-        description: reference fasta file - must be unzipped
+        description: (optional for BAM, required for CRAM) reference fasta file - must be unzipped
         pattern: "*.fasta"
         ontologies:
           - edam: "http://edamontology.org/format_1929" # FASTA

modules/nf-core/parabricks/fq2bam/tests/main.nf.test

@@ -137,6 +137,86 @@ nextflow_process {
         }
     }
 
+    test("SRR389222 - fastq - se - no reference") {
+
+        config './nextflow.config'
+
+        when {
+            params {
+                module_args = '--low-memory'
+                // Ref: https://forums.developer.nvidia.com/t/problem-with-gpu/256825/6
+                // Parabricks’s fq2bam requires 24GB of memory.
+                // Using --low-memory for testing
+                bwa_prefix = 'genome.fa'
+            }
+            process {
+                """
+                input[0] = Channel.of([
+				    [ id:'test', single_end:true ], // meta map
+				    [
+				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				    ]
+				])
+                input[1] = [ [], [] ]
+				input[2] = BWA_INDEX.out.index
+                input[3] = [ [], [] ]
+                input[4] = [ [], [] ]
+                input[5] = 'bam'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    file(process.out.bai[0][1]).name,
+                    process.out.versions,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+
+    test("SRR389222 - fastq - se - no reference - stub") {
+
+        options '-stub'
+
+        when {
+            params {
+                module_args = ''
+                bwa_prefix = ''
+            }
+            process {
+                """
+                input[0] = Channel.of([
+				    [ id:'test', single_end:true ], // meta map
+				    [
+				        file('https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', checkIfExists: true)
+				    ]
+				])
+                input[1] = [ [], [] ]
+				input[2] = BWA_INDEX.out.index
+                input[3] = [ [], [] ]
+                input[4] = [ [], [] ]
+                input[5] = 'bam'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions.get(0)).yaml,
+                    path(process.out.compatible_versions.get(0)).yaml
+                    ).match() }
+            )
+        }
+    }
+
     test("sarscov2 - fastq - pe") {
 
         when {

modules/nf-core/parabricks/fq2bam/tests/main.nf.test.snap

@@ -235,6 +235,105 @@
         },
         "timestamp": "2025-10-13T16:48:32.435485918"
     },
+    "SRR389222 - fastq - se - no reference - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+
+                ],
+                "5": [
+
+                ],
+                "6": [
+
+                ],
+                "7": [
+                    "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e"
+                ],
+                "8": [
+                    "versions.yml:md5,0c47791a7efece8e797f064b663ef855"
+                ],
+                "bai": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bam": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "bqsr_table": [
+
+                ],
+                "compatible_versions": [
+                    "compatible_versions.yml:md5,01a6599f855da953f58c26a0c1df301e"
+                ],
+                "crai": [
+
+                ],
+                "cram": [
+
+                ],
+                "duplicate_metrics": [
+
+                ],
+                "qc_metrics": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,0c47791a7efece8e797f064b663ef855"
+                ]
+            },
+            {
+                "PARABRICKS_FQ2BAM": {
+                    "pbrun": "4.6.0-1"
+                }
+            },
+            {
+                "PARABRICKS_FQ2BAM": null,
+                "pbrun_version": "4.6.0-1",
+                "compatible_with": "BWA mem: 0.7.15, Picard: 2.18.25"
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-31T18:59:39.126259477"
+    },
     "sarscov2 - fastq - pe - cram - stub": {
         "content": [
             {
@@ -347,5 +446,24 @@
             "nextflow": "25.04.8"
         },
         "timestamp": "2025-10-13T16:46:33.272405432"
+    },
+    "SRR389222 - fastq - se - no reference": {
+        "content": [
+            "3d5b94990c7fdf90a682edb5ee0f59de",
+            "test.bam.bai",
+            [
+                "versions.yml:md5,0c47791a7efece8e797f064b663ef855"
+            ],
+            {
+                "PARABRICKS_FQ2BAM": {
+                    "pbrun": "4.6.0-1"
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.8"
+        },
+        "timestamp": "2025-10-31T19:22:35.643220011"
     }
 }