longraredisease/conf/test.config at d603bf312611311d725963f615b75313b18ab1ee · nourmahfel/longraredisease · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
executor {
    name   = 'local'
    cpus   = 12
    memory = '24.GB'
    queueSize = 10
}

process {
    // 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
    }
}


params {
    // ========================================
    // MAIN ANALYSIS TOGGLES
    // ========================================
    input                       = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/samplesheet_ubam.csv"
    input_type                  = 'ubam'      // Skip alignment step if input BAM/CRAM files are already aligned
    sequencing_platform         = 'ont'   // Sequencing platform (e.g. 'ont', 'hifi', 'pacbio'). You can also define the parameters through the minimap2_model or winnowmap_model
    minimap2_model              = null
    use_winnowmap               = false  // Use Winnowmap for alignment instead of Minimap2
    winnowmap_model             = null
    haplotag_bam                = true
    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
    generate_coverage_report    = true       // Enable generation of coverage statistics
    sv                          = true      // Enable structural variant calling
    merge_sv                    = false
    snv                         = true       // Enable SNV calling
    cnv                         = true // Enable CNV calling with HiFiCNV if cnv_spectre is false
    str                         = true      // Enable STR analysis
    qc                          = true       // Enable quality control
    methyl                      = true       // Enable methylation calling
    fasta_file                  = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/genome_22/genome_22.fasta"
    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         = null
    outdir                      = './results'
    annotate_sv                 = false
    unify_vcf                   = false

    hificnv_exclude_bed        = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/hificnv/test.exclude.bed"
    hificnv_expected_cn_bed    = null // BED file with expected CNVs for HiFiCNV evaluation

    // Spectre test parameters
    use_test_data                = true // Use test data for Spectre - can not run it in test pipeline because does not accept subset of data.
    spectre_test_summary_txt     = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/spectre/test.mosdepth.summary.txt"
    spectre_test_regions_bed     = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/spectre/test.regions.bed.gz"
    spectre_test_regions_csi     = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/spectre/test.regions.bed.gz.csi"
    spectre_test_fasta_file      = "s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
    spectre_test_clair3_vcf      = "https://raw.githubusercontent.com/nf-core/test-datasets/longraredisease/spectre/test_clair3.vcf.gz"

}