SIP/nextflow.config at master · chansigit/SIP · 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
/*
          _____                    _____                    _____
         /\    \                  /\    \                  /\    \
        /::\    \                /::\    \                /::\    \
       /::::\    \               \:::\    \              /::::\    \
      /::::::\    \               \:::\    \            /::::::\    \
     /:::/\:::\    \               \:::\    \          /:::/\:::\    \
    /:::/__\:::\    \               \:::\    \        /:::/__\:::\    \
    \:::\   \:::\    \              /::::\    \      /::::\   \:::\    \
  ___\:::\   \:::\    \    ____    /::::::\    \    /::::::\   \:::\    \
 /\   \:::\   \:::\    \  /\   \  /:::/\:::\    \  /:::/\:::\   \:::\____\
/::\   \:::\   \:::\____\/::\   \/:::/  \:::\____\/:::/  \:::\   \:::|    |
\:::\   \:::\   \::/    /\:::\  /:::/    \::/    /\::/    \:::\  /:::|____|
 \:::\   \:::\   \/____/  \:::\/:::/    / \/____/  \/_____/\:::\/:::/    /
  \:::\   \:::\    \       \::::::/    /                    \::::::/    /
   \:::\   \:::\____\       \::::/____/                      \::::/    /
    \:::\  /:::/    /        \:::\    \                       \::/____/
     \:::\/:::/    /          \:::\    \                       ~~
      \::::::/    /            \:::\    \
       \::::/    /              \:::\____\
        \::/    /                \::/    /
         \/____/                  \/____/


                  __ _
                 / _(_)
  ___ ___  _ __ | |_ _  __ _ ___
 / __/ _ \| '_ \|  _| |/ _` / __|
| (_| (_) | | | | | | | (_| \__ \
 \___\___/|_| |_|_| |_|\__, |___/
                        __/ |
                       |___/
*/

// basic inputs and outputs
params.cellhome    = "/data/hca/chensijie/Dataset/SMART1/FASTQfilesSub"
params.output      = "/data/hca/chensijie/Result/SubSMART1_Result"

// analysis step configs
params.readqc      = "fastp"
params.quant       = "salmon"
params.quant_unit  = "count"
params.downstream  = "seurat"


// notification options
params.use_email   = false
params.email       = "chensj16@mails.tsinghua.edu.cn"

// modifiable built-in options
/// Reference
params.salmon_index="/data/hca/chensijie/Reference/transcriptome/SALMON21_Homo_sapiens.GRCh38.cdna.all"
params.tx2gene = "/data/hca/chensijie/code/SIP/scripts/tx2gene.SALMON21_Homo_sapiens.GRCh38.cdna.all.tsv"


// Seurat Analysis Parameters
params.seuratMinCells = "1"
params.seuratMinGenes = "200"
params.seuratNGeneLowerBound = "200"
params.seuratNGeneUpperBound = "Inf"
params.seuratMitoLowerBound  = "-Inf"
params.seuratMitoUpperBound  = "0.30"
params.seuratSubgroupResolution = "1.03"
params.seuratTSNEPerplexity  = "4"
params.seuratDEGeneKept      = "10"
params.seuratDEGeneViz       = "3"
params.seuratDEMinDetectRatio= "0.15"
params.seuratDEpvalCut       = "0.05"


process{

    container= 'sunhao2018/centos_docker_test:latest'


}


docker{
    enabled=true
    fixOwnership=true
}