Add tests

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
@@ -24,8 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }
         memory = { 5.GB * task.attempt }

conf/modules.config

@@ -65,7 +65,7 @@ process {
             path: { "${params.outdir}/${meta.id}/filtered_bam" },
             mode: 'copy'
         ]
-        cpus = 4  // Set the number of CPUs here
+        cpus = 4
     }
 
 
@@ -92,7 +92,6 @@ process {
             hifi: 'map-hifi',
             pacbio: 'map-pb'
         ]
-        // Use manual model if provided, otherwise use platform-based preset
         def preset = params.minimap2_model ?: (presets[params.sequencing_platform] ?: 'map-ont')
         "-Y -y -ax ${preset} -R '@RG\\tID:${meta.id}\\tSM:${meta.id}\\tPL:${params.sequencing_platform.toUpperCase()}'"
     }
@@ -477,32 +476,25 @@ process {
 
     withName: 'DEEPVARIANT_RUNDEEPVARIANT' {
     ext.args = {
-        // Define model type presets based on sequencing platform
         def model_types = [
             ont: 'ONT_R104',
             hifi: 'PACBIO',
             pacbio: 'PACBIO',
         ]
         def model_type = model_types[params.sequencing_platform] ?: 'ONT_R104'
 
-        // Build arguments list
-        def args_list = [
+        def regions_arg = ""
+        if (params.deepvariant_regions) {
+            regions_arg = "--regions=${params.deepvariant_regions}"
+        }
+
+        return [
             "--model_type=${model_type}",
             "--sample_name=${meta.id}",
-            "--regions=${params.deepvariant_regions}",
+            regions_arg,
             "--make_examples_extra_args=${params.deepvariant_make_examples_extra_args}"
-        ]
-
-        return args_list.findAll { it }.join(' ').trim()
+        ].findAll { it }.join(' ').trim()
     }
-
-    ext.prefix = { "${meta.id}_deepvariant" }
-
-    publishDir = [
-        path: { "${params.outdir}/${meta.id}/deepvariant" },
-        mode: 'copy'
-    ]
-
     }
 
     withName: 'DEEPVARIANT_VCFSTATSREPORT'{

conf/test.config

@@ -4,18 +4,49 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 executor {
-    name = 'local'
-    cpus = 8
-    memory = '16.GB'
+    name   = 'local'
+    cpus   = 12
+    memory = '24.GB'
     queueSize = 10
 }
+
 process {
-    resourceLimits = [
-        cpus: 1,
-        memory: '10.GB'
-    ]
+    // nf-core standard process labels
+    withLabel: 'process_single' {
+        cpus   = 1
+        memory = 2.GB
+        time   = 4.h
+    }
+    withLabel: 'process_low' {
+        cpus   = 2
+        memory = 4.GB
+        time   = 6.h
+    }
+    withLabel: 'process_medium' {
+        cpus   = 2      // ← REDUCED from 4
+        memory = 4.GB   // ← REDUCED from 8
+        time   = 8.h
+    }
+    withLabel: 'process_high' {
+        cpus   = 4      // ← REDUCED from 8
+        memory = 8.GB   // ← REDUCED from 16
+        time   = 10.h
+    }
+
+    // CRITICAL: Force MINIMAP2_ALIGN to use minimal resources
+    withName: 'MINIMAP2_ALIGN' {
+        cpus   = 2
+        memory = 4.GB
+        // Now 4 samples can run in parallel: 8 CPUs / 2 = 4 parallel tasks
+    }
+
+    withName: 'MINIMAP2_INDEX' {
+        cpus   = 2
+        memory = 4.GB
+    }
 }
-trace.fields = "task_id,hash,native_id,script"
+
+
 
 params {
     // ========================================
@@ -28,7 +59,7 @@ params {
     use_winnowmap               = false  // Use Winnowmap for alignment instead of Minimap2
     winnowmap_model             = null
     haplotag_bam                = true
-    trio_analysis               = false  // Enable trio analysis for SNV calling and phasing
+    trio_analysis               = true  // Enable trio analysis for SNV calling and phasing
     filter_targets              = false    // Enable filtering of alignments to target regions (e.g. for gene panels or exomes)
     targets_bed                 = null
     generate_bam_stats          = true       // Enable generation of BAM statistics
@@ -44,7 +75,7 @@ params {
     straglr_bed                 = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/straglr/str.test.bed"
     trgt_bed                    = "${projectDir}/assets/data/trgt_repeat_catalog.hg38.bed"
     chromosome_codes            = ['chr22']
-    deepvariant_regions         = 'chr22'
+    deepvariant_regions         = null
     outdir                      = './results'
     annotate_sv                 = false
     unify_vcf                   = false

fix_editorconfig.py

@@ -100,7 +100,7 @@ def fix_nextflow_formatting(filepath):
     'assets/snpeff_db.txt',
     'nextflow.config',
     'conf/modules.config',
-    'modules/local/svim/alignment/tests/main.nf.test',
+    'modules/local/spectre/cnvcaller/main.nf',
     'subworkflows/local/call_str/tests/main.nf.test',
     'subworkflows/local/annotate_sv/main.nf',
     'subworkflows/local/align/main.nf',

modules.json

@@ -210,6 +210,11 @@
                         "git_sha": "72717e1f3feabaa57a6a71ba5a85d9c4ceeba514",
                         "installed_by": ["modules"]
                     },
+                    "svim/alignment": {
+                        "branch": "master",
+                        "git_sha": "040e62715d9e5a54c962338426e02718f19abee6",
+                        "installed_by": ["modules"]
+                    },
                     "tabix/bgzip": {
                         "branch": "master",
                         "git_sha": "f2cfcf9d3f6a2d123e6c44aefa788aa232204a7a",

modules/local/spectre/cnvcaller/main.nf

@@ -2,11 +2,12 @@ process SPECTRE_CNVCALLER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "${moduleDir}/environment.yml"
-    container "ghcr.io/nourmahfel/spectre-ont:0.3.2"
+    // FIXME Conda is not supported at the moment
+
+    container "community.wave.seqera.io/library/ont-spectre:0.3.2--adfae189059be3d9"
 
     input:
-    tuple val(meta), path(summary), path(regions_bed), path(regions_csi), path(vcf)
+    tuple val(meta), path(mosdepth_summary), path(mosdepth_regions_bed), path(mosdepth_regions_csi), path(vcf)
     tuple val(meta2), path(fasta)
     path(metadata_file)
     path(blacklist)
@@ -18,7 +19,7 @@ process SPECTRE_CNVCALLER {
     tuple val(meta), path("*.spc.gz")                    , emit: spc
     tuple val(meta), path("predicted_karyotype.txt")     , emit: txt
     tuple val(meta), path("windows_stats", type: 'dir')  , emit: winstats
-    path "versions.yml"                                  , emit: versions
+    tuple val("${task.process}"), val('spectre'), eval('spectre version 2>&1 | grep -oP "Spectre version: \\K[0-9.]+"'), emit: versions_spectre, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,26 +33,21 @@ process SPECTRE_CNVCALLER {
     mkdir -p ${coverage_dir}
 
     # Stage the mosdepth files into the directory with proper naming
-    cp -L ${summary} ${coverage_dir}/${meta.id}.mosdepth.summary.txt
-    cp -L ${regions_bed} ${coverage_dir}/${meta.id}.regions.bed.gz
-    cp -L ${regions_csi} ${coverage_dir}/${meta.id}.regions.bed.gz.csi
+    cp -L ${mosdepth_summary} ${coverage_dir}/${meta.id}.mosdepth.summary.txt
+    cp -L ${mosdepth_regions_bed} ${coverage_dir}/${meta.id}.regions.bed.gz
+    cp -L ${mosdepth_regions_csi} ${coverage_dir}/${meta.id}.regions.bed.gz.csi
 
     # Now run spectre with the directory - use bin_size input parameter, not params
     spectre CNVCaller \\
         --coverage ${coverage_dir} \\
         --snv ${vcf} \\
         --reference ${fasta} \\
         --output-dir . \\
-        --sample-id=${prefix} \\
         --metadata ${metadata_file} \\
         --blacklist ${blacklist} \\
         --bin-size ${bin_size} \\
         ${args}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        spectre: \$(spectre --version 2>&1 | grep -oP 'version \\K[0-9.]+' || spectre --help 2>&1 | grep -oP 'v[0-9.]+' | sed 's/v//' || echo "1.0.0")
-    END_VERSIONS
     """
 
     stub:
@@ -63,9 +59,5 @@ process SPECTRE_CNVCALLER {
     touch predicted_karyotype.txt
     mkdir windows_stats
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        spectre: 0.3.2
-    END_VERSIONS
     """
 }