add dragen bam to output

modules/UMCUGenetics/dragen/main.nf

@@ -9,15 +9,15 @@ process DRAGEN {
     container '079623148045.dkr.ecr.eu-central-1.amazonaws.com/cp-prod/f1b7ad6a-11ac-4bc1-b705-b275ff2887ad:latest'
 
     input:
-    // TODO: Move ref_tar unpacking to a separate process to avoid unpacking the reference for every sample? -> added in prs branch
     tuple val(meta), path(r1_fastq), path(r2_fastq)
     path fastq_list
-    path ref_tar
+    tuple val(meta2), path(ref_dir)
     path repeat_genotype_specs
 
     output:
     tuple val(meta), path("*"), emit: output
     tuple val(meta), path('*.csv'), emit: csv
+    tuple val(meta), path("${prefix}.bam"), path("${prefix}.bam.bai"), emit: bam_bai
     tuple val(meta), path("${prefix}.wgs_coverage_metrics.csv"), optional: true, emit: wgs_coverage_metrics
     tuple val(meta), path("${prefix}.cnv_metrics.csv"), optional: true, emit: cnv_metrics
     tuple val(meta), path("${prefix}.mapping_metrics.csv"), optional: true, emit: mapping_metrics
@@ -31,24 +31,18 @@ process DRAGEN {
     script:
     prefix = task.ext.prefix ?: "${meta.id}"
     def args = task.ext.args ?: ''
-
-    if (repeat_genotype_specs) {
-        args = args + " --repeat-genotype-enable true --repeat-genotype-specs " + repeat_genotype_specs
-    }
-
+    def repeat_specs = repeat_genotype_specs ? "--repeat-genotype-enable true --repeat-genotype-specs ${repeat_genotype_specs}" : ""
     """
-    mkdir -p /scratch/reference
-    tar -C /scratch/reference -xf ${ref_tar}
-
     /opt/edico/bin/dragen --partial-reconfig HMM --ignore-version-check true
 
     /opt/edico/bin/dragen --lic-instance-id-location /opt/instance-identity \\
-        --ref-dir /scratch/reference/DRAGEN/9 \\
+        --ref-dir ${ref_dir} \\
         --fastq-list ${fastq_list} \\
         --fastq-list-sample-id ${meta.id} \\
         --output-file-prefix ${prefix} \\
         --output-directory ./ \\
         --intermediate-results-dir /scratch \\
+        ${repeat_specs} \\
         ${args}
     """
 
@@ -59,6 +53,7 @@ process DRAGEN {
     echo ${args}
 
     touch ${prefix}.bam
+    touch ${prefix}.bam.bai
     touch ${prefix}.wgs_coverage_metrics.csv
     touch ${prefix}.cnv_metrics.csv
     touch ${prefix}.mapping_metrics.csv

modules/UMCUGenetics/dragen/tests/main.nf.test

@@ -6,8 +6,34 @@ nextflow_process {
 
     tag "modules"
     tag "modules_UMCUGenetics"
+    tag "subworkflows/prepare_ica_references"
     tag "dragen"
 
+
+    setup{
+        nfcoreInitialise("${launchDir}/library/")
+        nfcoreInstall(
+            "${launchDir}/library/",
+            [
+                "samtools/faidx",
+                "gatk4/createsequencedictionary"
+            ]
+        )
+        nfcoreLink("${launchDir}/library/", "${baseDir}/modules/")
+
+        run("PREPARE_ICA_REFERENCES") {
+                script "../../../../subworkflows/UMCUGenetics/prepare_ica_references/main.nf"
+                workflow {
+                    """
+                    input[0] = channel.of([
+                        [id: 'genome'],
+                        file(params.subworkflows_umcu_testdata_base_path + "prepare_ica_references/genome.tar.gz", checkIfExists: true)
+                    ])
+                    """
+                }
+            }
+    }
+
     test("dragen - stub") {
         options '-stub'
         when {
@@ -19,7 +45,7 @@ nextflow_process {
                     []
                 ]
                 input[1] = []
-                input[2] = []
+                input[2] = PREPARE_ICA_REFERENCES.out.genome_dir
                 input[3] = []
                 """
             }
@@ -33,5 +59,8 @@ nextflow_process {
                 ).match() }
             )
         }
+        cleanup {
+            nfcoreUnlink("${launchDir}/library/", "${baseDir}/modules/")
+        }
     }
 }

modules/UMCUGenetics/dragen/tests/main.nf.test.snap

@@ -9,6 +9,7 @@
                         },
                         [
                             "sample1.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sample1.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.cnv_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.gvcf_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.mapping_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -36,48 +37,66 @@
                         {
                             "id": "sample1"
                         },
-                        "sample1.wgs_coverage_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample1.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sample1.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "3": [
                     [
                         {
                             "id": "sample1"
                         },
-                        "sample1.cnv_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample1.wgs_coverage_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "4": [
                     [
                         {
                             "id": "sample1"
                         },
-                        "sample1.mapping_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample1.cnv_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "5": [
                     [
                         {
                             "id": "sample1"
                         },
-                        "sample1.ploidy_estimation_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample1.mapping_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "6": [
                     [
                         {
                             "id": "sample1"
                         },
-                        "sample1.gvcf_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample1.ploidy_estimation_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "7": [
+                    [
+                        {
+                            "id": "sample1"
+                        },
+                        "sample1.gvcf_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "8": [
                     [
                         "DRAGEN",
                         "dragen",
                         "bash: line 1: dragen: command not found"
                     ]
                 ],
+                "bam_bai": [
+                    [
+                        {
+                            "id": "sample1"
+                        },
+                        "sample1.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                        "sample1.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "cnv_metrics": [
                     [
                         {
@@ -123,6 +142,7 @@
                         },
                         [
                             "sample1.bam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "sample1.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.cnv_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.gvcf_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
                             "sample1.mapping_metrics.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
@@ -165,10 +185,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-08-18T11:08:58.003281",
+        "timestamp": "2026-08-28T16:31:56.534107",
         "meta": {
             "nf-test": "0.9.5",
-            "nextflow": "25.10.2"
+            "nextflow": "26.04.6"
         }
     }
 }

modules/UMCUGenetics/untar/genome/main.nf

@@ -1,24 +1,46 @@
 process UNTAR_GENOME {
-    tag "${archive}"
+    tag "${meta.id}"
     label 'process_single'
 
     container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
         ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/52/52ccce28d2ab928ab862e25aae26314d69c8e38bd41ca9431c67ef05221348aa/data'
         : 'community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8'}"
 
     input:
-    tuple val(meta), path(archive)
+    tuple val(meta), path(genome_tar)
 
     output:
-    tuple val(meta), path('genome'), emit: untar
+    tuple val(meta), path('dragen_ref'),   emit: dragen_ref
+    tuple val(meta), path('genome.fa'),    emit: fasta
+    tuple val(meta), path("genes.gtf.gz"), emit: gtf
     tuple val("${task.process}"), val('UNTAR'), eval('echo 1.0.0'), emit: versions_untar_genome, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def hashtable_version = params.dragen_hashtable_version ?: ''
     """
-    mkdir genome
-    tar -xavf ${archive} -C genome
+    tar -xzf ${genome_tar}
+    mapfile -t hts < <(find . -name hash_table.cfg -printf '%h\\n' | grep -E '/[0-9]+\$' | sort -V)
+
+    if [ \${#hts[@]} -eq 0 ]; then
+        echo "ERROR: no DRAGEN hashtable (hash_table.cfg) found in ${genome_tar}" >&2
+        exit 1
+    fi
+
+
+    if [ -n "${hashtable_version}" ]; then
+        ref_dir=\$(printf '%s\\n' "\${hts[@]}" | grep -E "/${hashtable_version}\$") || {
+            echo "ERROR: hashtable v${hashtable_version} not found. Available: \${hts[*]}" >&2
+            exit 1
+        }
+    else
+        ref_dir=\${hts[-1]}          # Highest version
+    fi
+
+    echo "Using DRAGEN ref-dir: \$ref_dir" >&2
+    ln -s "\$(realpath \$ref_dir)" dragen_ref
+
     """
 }

modules/UMCUGenetics/untar/genome/tests/main.nf.test

@@ -15,14 +15,17 @@ nextflow_process {
                 """
                 input[0] = channel.of([
                     [id: 'genome'],
-                    file(params.subworkflows_umcu_testdata_base_path + "prepare_ica_references/genome.tar", checkIfExists: true)
+                    file(params.subworkflows_umcu_testdata_base_path + "prepare_ica_references/genome.tar.gz", checkIfExists: true)
                 ])
                 """
             }
         }
         then{
             assertAll(
                 { assert process.success },
+                { assert path(process.out.dragen_ref[0][1]).exists() },
+                { assert path(process.out.fasta[0][1]).exists() },
+                { assert path(process.out.gtf[0][1]).exists() },
                 { assert snapshot(
                     process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() }

modules/UMCUGenetics/untar/genome/tests/main.nf.test.snap

@@ -11,7 +11,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-08-21T11:44:44.991954",
+        "timestamp": "2026-08-28T10:56:51.250213",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.6"

subworkflows/UMCUGenetics/bam_prs/nextflow.config

@@ -44,7 +44,6 @@ process {
         cpus = 2
 		memory = { 10.GB * task.attempt }
 		time = { 30.m * task.attempt }
-        array = params.job_array_size
         ext.args = {
 			[
 				"--allow-extra-chr",

subworkflows/UMCUGenetics/prepare_ica_references/main.nf

@@ -11,23 +11,18 @@ workflow PREPARE_ICA_REFERENCES {
 
     UNTAR_GENOME(genome_tar)
 
-    genome_fasta = UNTAR_GENOME.out.untar
-        .map{ meta, dir -> [meta, file("${dir}/genome.fa",
-                    checkIfExists: !workflow.stubRun)
-            ]}
-
     SAMTOOLS_FAIDX(
-        genome_fasta.map {meta, fasta -> [meta, fasta, []]},
+        UNTAR_GENOME.out.fasta.map {meta, fasta -> [meta, fasta, []]},
         false
     )
 
-    GATK4_CREATESEQUENCEDICTIONARY(genome_fasta)
+    GATK4_CREATESEQUENCEDICTIONARY(UNTAR_GENOME.out.fasta)
 
 
     emit:
-    genome_fasta = genome_fasta
+    genome_fasta = UNTAR_GENOME.out.fasta
     genome_fai   = SAMTOOLS_FAIDX.out.fai
     genome_dict  = GATK4_CREATESEQUENCEDICTIONARY.out.dict
-    genome_dir   = UNTAR_GENOME.out.untar
+    genome_dir   = UNTAR_GENOME.out.dragen_ref
 
 }

subworkflows/UMCUGenetics/prepare_ica_references/tests/main.nf.test

@@ -24,24 +24,24 @@ nextflow_workflow {
     }
 
     test("Validate genome untar and processing") {
+        options "-stub"
         when{
             workflow{
                 """
                 input[0] = channel.of([
                 [id: 'genome'],
-                    file(params.subworkflows_umcu_testdata_base_path + "prepare_ica_references/genome.tar", checkIfExists: true)
+                    file(params.subworkflows_umcu_testdata_base_path + "prepare_ica_references/genome.tar.gz", checkIfExists: true)
                 ])
                 """
             }
         }
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(
-                    workflow.out.genome_fasta,
-                    workflow.out.genome_fai,
-                    workflow.out.genome_dict
-                ).match()}
+                { assert path(workflow.out.genome_fasta[0][1]).exists() },
+                { assert path(workflow.out.genome_fai[0][1]).exists() },
+                { assert path(workflow.out.genome_dict[0][1]).exists() },
+                { assert path(workflow.out.genome_dir[0][1]).exists() },
             )
         }