simple/foo.nf at master · cahofer/simple · 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
#!/usr/bin/env nextflow


process foo {
  publishDir params.outdir

  input:
  val x

  output:
  path 'x.txt'

  """
  echo $x > x.txt

  """
}

/*
Python script to set up dp3 parset and copy to nodes according to pipeline
*/
process SetupSimulateVisibilities{
    publishDir params.outdir

    input:
    val ns
    val ne
    val copy_dir
    val indir
    val dp3_parset_file

    script:
    """
    for ni in {${ns}..${ne}}; do
        mkdir -p /net/node\${ni}/${copy_dir}
        cp -r ${indir}/${dp3_parset_file} /net/node\${ni}/${copy_dir}/${dp3_parset_file}
    done
    """
}

/*
Python script to set up noise parset according to pipeline
*/
params.outdir = "${launchDir}"

process SetupGaussianNoise{
    publishDir params.outdir, mode: 'copy'

    input:
    val datapath
    val msprefix
    val skymodel_path
    val outcol
    val noise_parset

    output:
    path noise_parset

    script:
    """
    python3 /home/users/cahofer/code/simple/scripts/setup_noise.py -d ${datapath} -m ${msprefix} -s ${skymodel_path} -c ${outcol} -n ${noise_parset}
    """
}

/*
Bash script to make the machines file for sagecal.
*/
process MakeMachinesFile {
    publishDir params.outdir, mode: 'copy'

    input:
    val ns
    val ne

    output:
    path "machines.txt"

    script:
    """
    seq  -f "node%g.fast.dawn.rug.nl slots=4 max_slots=4" ${ns} ${ne} > machines.txt
    """
}

process MSList {
    publishDir params.outdir, mode: 'copy'

    input:
    val msprefix
    val copy_dir
    val ns
    val ne

    output:
    path "file_list_${msprefix}"

    script:
    """
    for ni in {$ns..$ne}; do
        ls -d /net/node\${ni}/${copy_dir}/${msprefix}*.MS >> file_list_${msprefix}
    done
    """
}