PoolSeqFlow/parameters.config.template at main · ozankiratli/PoolSeqFlow · 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
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
params {
    //main parameters
    mainDir         = 'Project'
    dataSource      = 'Data'
    readPattern     = "*_R{1,2}.fq.gz"
    referenceFile   = 'dmel-all-chromosome-r6.61.fasta.gz'
    gffFile         = 'dmel-all-r6.61.gff.gz'
    rgTagsFile      = 'RGTags.csv'
    poolSize        = 100
    threads         = 4

    referencePath   = "${mainDir}/${params.referenceFile}"
    gffPath         = "${mainDir}/${params.gffFile}"

    // directories
    dir {
        data            = "${mainDir}/${params.dataSource}"
        outputs         = "${mainDir}/Output"
        references      = "${mainDir}/Reference"
        scripts         = "${mainDir}/scripts"
        reports         = "${mainDir}/Reports"
        bin             = "${mainDir}/bin"
        logs            = "${mainDir}/Logs"
        snpEff          = "${params.dir.references}/snpEff"

        output {
            aligned         = "${params.dir.outputs}/Aligned"
            ready           = "${params.dir.outputs}/Ready"
            trimmed         = "${params.dir.outputs}/Trimmed"
            unpaired        = "${params.dir.outputs}/Unpaired"
            vcf             = "${params.dir.outputs}/VCF"
            freq            = "${params.dir.outputs}/Frequencies"
            reports         = "${params.dir.outputs}/Reports"
            temp            = "${params.dir.outputs}/Temp"

            report {
                align           = "${params.dir.output.reports}/Align"
                coverage        = "${params.dir.output.reports}/Coverage"
                fastqc          = "${params.dir.output.reports}/Fastqc"
                trim            = "${params.dir.output.reports}/Trim"
            }
        }

        report {
            align           = "${params.dir.reports}/Align"
            coverage        = "${params.dir.reports}/Coverage"
            fastqc          = "${params.dir.reports}/Fastqc"
            trim            = "${params.dir.reports}/Trim"
            clean           = "${params.dir.reports}/Clean"
        }
    }

    // setting reference and data full paths
    reference       = "${params.dir.references}/${params.referenceFile.replace('.gz', '')}"
    gff             = "${params.dir.references}/${params.gffFile.replace('.gz', '')}"
    reads           = "${params.dir.data}/${params.readPattern}"

    // java parameters
    java {
        heapSize        = '-Xmx8g'
        garbageCollect  = '-XX:ParallelGCThreads=4'
        options         = "${params.java.heapSize} ${params.java.garbageCollect}"
    }

    // fastqc parameters
    fastqc {
        threads         = 2
        memory          = "2G"
        options         = "-t ${params.fastqc.threads} --memory ${params.fastqc.memory}"
    }

    // trim_galore parameters
    trim_galore {
        threads         = 4
        quality         = 25
        adapter1        = 'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT'
        adapter2        = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG'
        options         = "--cores ${params.trim_galore.threads} --fastqc --fastqc_args \"${params.fastqc.options}\" --paired --retain_unpaired -q ${params.trim_galore.quality} -a ${params.trim_galore.adapter1} -a2 ${params.trim_galore.adapter2}"
    }

    cutadapt {
        threads        = 2   // 0 means autodetect
        at_gc_error    = 0.025
        min_length     = 50
        options        = "--cores ${params.cutadapt.threads}"
        //options        = "--cores ${params.cutadapt.threads} -q ${params.trim_galore.quality} --minimum-length ${params.cutadapt.min_length}"
    }

    // BWA parameters
    bwa {
        threads         = 8
        minScoreOutput  = 30
        batchSize       = 10000000
        options         = "-t ${params.bwa.threads} -K ${params.bwa.batchSize} -T ${params.bwa.minScoreOutput}"
    }

    // Samtools parameters
    samtools {
        threads         =  "${params.threads - 1}"
        filter          = "0xF0C"       // See `man samtools-flags` for more information
        required        = "0x2"         // See `man samtools-flags` for more information
        mapq            = 30
        rgTagsFile      = "${params.mainDir}/${params.rgTagsFile}"
    }


    // bcftools parameters
    bcftools {
        scaleMapQ       = 50
        baseQualMin     = 30
        varQualMin      = 30
        maxDepth        = 2000
        mpileupOptions  = "-B -C ${params.bcftools.scaleMapQ} -q ${params.bcftools.baseQualMin} -Q ${params.bcftools.varQualMin} -d ${params.bcftools.maxDepth} -a AD,DP,SP,INFO/AD -Ou"

        callOptions         = "-m -A -v -Ov"
    }

    // VCF parameters
    vcf {
        fileName        = 'Test'
    }

    // vcf Filtering parameters
    vcftools {
        minDP           = 100
        minQUAL         = 30
        maxMissing      = 1.0
    }

    // Filter False Positives parameters
    filterFalsePositives {
        sensitivity     = 1.0 / (2 * params.poolSize)
        sampleThreshold = 0.2
    }

    // SNPEff parameters
    snpEff {
        db              = 'dmel-all-r6.61'  // Drosophila melanogaster database
        config          = "snpEff.config"
        buildOptions    = "-gff3 -noCheckCds -noCheckProtein -v"
        options         = "-v -stats ${params.dir.reports}/snpeff_summary.html"
    }

    // Add software commands
    software {
        java            = 'java'
        cutadapt        = 'cutadapt'
        fastqc          = 'fastqc'
        trim_galore     = 'trim_galore'
        samtools        = 'samtools'
        bamtools        = 'bamtools'
        bwa             = 'bwa'
        bcftools        = 'bcftools'
        vcftools        = 'vcftools'
        snpEff          = 'snpEff'
    }
}