nf-atac/nextflow.config at main · cellgeni/nf-atac · 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
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
// Nextflow flags
nextflow.enable.moduleBinaries = true

// Pipeline parameters
params {
    // required input params
    sample_table     = null
    celltypes        = null
    pseudobulk_peaks = null
    atac_adata       = null
    callPeaks        = null
    inferConsensus   = null
    attachGEX        = null
    chromsizes       = "${projectDir}/reference/hg38.chrom.sizes"
    blacklist        = "${projectDir}/reference/hg38-blacklist.v2.bed"
    tss_bed          = "${projectDir}/reference/hg38_pycistopic_tss.bed"

    // optional params
    help         = false
    output_dir   = 'results'
    publish_mode = 'link'

    // pyCISTOPIC params
    cistopic {
        // pseudobulking
        normalize_bigwig = true
        // peak calling
        specie           = 'hs'
        input_format     = 'BEDPE'
        shift            = 73
        extend_read_size = 146
        keep_duplicates  = 'all'
        q_value_cutoff   = 0.05
        // consensus
        peak_half_width = 250
        // quality control
        tss_flank_window             = 2000
        tss_smoothing_rolling_window = 10
        tss_window                   = 50
        tss_min_norm                 = 0.2
        min_fragments_per_cb         = 10
        use_pyranges                 = false
        dont_collapse_duplicates     = false
        // create object
        min_frag                 = 1
        min_cell                 = 1
        is_acc                   = 1
        split_pattern            = '___'
        check_for_duplicates     = true
        use_automatic_thresholds = true
    }
}

// Unscoped options
outputDir = params.output_dir
cleanup   = false
workDir   = "nf-work"

process {
    queue         = 'normal'
    maxRetries    = 5
    errorStrategy = { task.exitStatus in 130..140 ? 'retry' : 'finish' }
}

// Load config for cisTopic component
includeConfig 'configs/cistopic_countfragments.config'
includeConfig 'configs/cistopic_splitannotation.config'
includeConfig 'configs/cistopic_pseudobulk.config'
includeConfig 'configs/cistopic_callpeaks.config'
includeConfig 'configs/cistopic_inferconsensus.config'
includeConfig 'configs/cistopic_qualitycontrol.config'
includeConfig 'configs/cistopic_createobject.config'
includeConfig 'configs/cistopic_combineobjects.config'
includeConfig 'configs/anndata_concat.config'
includeConfig 'configs/anndata_attachcelltypes.config'
includeConfig 'configs/anndata_couplemultiome.config'
includeConfig 'configs/anndata_toh5ad.config'

singularity {
    enabled     = true
    autoMounts  = true
    pullTimeout = '120m'
    runOptions  = '-B /lustre,/nfs'
    cacheDir    = '/nfs/cellgeni/singularity/images/'
}

executor {
    name           = 'lsf'
    perJobMemLimit = true
}

// Capturing Nextflow log files into a 'reports' directory
import java.time.*
Date now = new Date()

params {
    tracedir  = "reports"
    timestamp = now.format("yyyyMMdd-HH-mm-ss")
}

timeline {
    enabled = true
    file    = "${params.tracedir}/${params.timestamp}_timeline.html"
}

report {
    enabled = true
    file    = "${params.tracedir}/${params.timestamp}_report.html"
}

trace {
    enabled = true
    file    = "${params.tracedir}/${params.timestamp}_trace.tsv"
}

// Manifest
manifest {
  name            = 'cellgeni/nf-atac'
  homePage        = 'https://github.com/cellgeni/nf-atac'
  description     = "Nextflow pipeline for single-cell ATAC-seq data processing and analysis"
  mainScript      = 'main.nf'
  nextflowVersion = '!>=25.04.4'
  version         = '25-280'
  defaultBranch   = 'main'
  contributors    = [
    [
      name: 'Aljes Binkevich',
      email: 'ab76@sanger.ac.uk',
      github: 'claptar',
      contribution: ['author', 'maintainer', 'contributor'],
    ],
    [
      name: 'Pavel Mazin',
      email: 'pm19@sanger.ac.uk',
      github: 'iaaka',
      contribution: ['author', 'maintainer', 'contributor'],
    ],
  ]
}