WorkflowAssembly/streamflow.yml at main · qBioTurin/WorkflowAssembly · 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
158
159
160
161
162
163
164
165
166
167
#!/usr/bin/env streamflow
version: v1.0
workflows:
  workflow:
    type: cwl
    config:
      file: workflow.cwl
      settings: config.yml
      docker:
        - step: /
          deployment:
            type: none
            config: {}
    bindings:
      - step: /assembly_evaluation/assembly/canu/canu
        target:
          deployment: c3sfr1-slurm
          service: canu
      - step: /assembly_evaluation/assembly/canu/medaka_canu
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/flye/flye
        target:
          deployment: c3sfr1-slurm
          service: flye
      - step: /assembly_evaluation/assembly/flye/medaka_flye
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/wtdbg2/wtdbg2
        target:
          deployment: c3sfr1-slurm
          service: wtdbg2
      - step: /assembly_evaluation/assembly/wtdbg2/wtpoa-cns
        target:
          deployment: c3sfr1-slurm
          service: wtdbg2
      - step: /assembly_evaluation/assembly/wtdbg2/medaka_wtdbg2
        target:
          deployment: c3sfr1-slurm
          service: medaka
      - step: /assembly_evaluation/assembly/quickmerge
        target:
          deployment: c3sfr1-slurm
          service: quickmerge
      - step: /assembly_evaluation/evaluation/busco
        target:
          deployment: c3sfr1-slurm
          service: busco
      - step: /assembly_evaluation/best-result
        target:
          deployment: c3sfr1-slurm
          service: best-result
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmodeler-buildDatabase
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmodeler-run
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatclassifier
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/repeatmasker
        target:
          deployment: c3sfr1-slurm
          service: repeatmodeler
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/transposonpsi
        target:
          deployment: c3sfr1-slurm
          service: transposonpsi
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/transposonpsi-bedtools
        target:
          deployment: c3sfr1-slurm
          service: bedtools
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/edta
        target:
          deployment: c3sfr1-slurm
          service: edta
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/transposon/vsearch
        target:
          deployment: c3sfr1-slurm
          service: vsearch
      - step: /assembly_evaluation/geneprediction/gene-prediction-prokaryotic
        target:
          deployment: c3sfr1-slurm
          service: prokka
      - step: /assembly_evaluation/evaluation-prediction/busco
        target:
          deployment: c3sfr1-slurm
          service: busco
      - step: /assembly_evaluation/geneprediction/gene-prediction-eukaryotic/gene-prediction-eukaryotic
        target:
          deployment: c3sfr1-slurm
          service: braker3
      - step: /assembly_evaluation/clean-proteins
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/interpro
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/go_enrich
        target:
          deployment: c3sfr1-slurm
          service: interpro
      - step: /assembly_evaluation/postprocessing
        target:
          deployment: c3sfr1-slurm
          service: postprocessing

database:
  type: sqlite
  config:
    connection: ./database/test

deployments:
  c3sfr1-ssh:
    type: ssh
    config:
      nodes:
        - c3sfr1.di.unito.it
      username: scontald
      sshKey: key/id_rsa
    workdir: /beegfs/home/scontald/sf/assembly
  c3sfr1-slurm:
    type: slurm
    config:
      maxConcurrentJobs: 40
      services:
        canu:
          file: sbatch/canu.sh
        flye:
          file: sbatch/flye.sh
        wtdbg2:
          file: sbatch/wtdbg2.sh
        medaka:
          file: sbatch/medaka.sh
        quickmerge:
          file: sbatch/quickmerge.sh
        busco:
          file: sbatch/busco.sh
        prokka:
          file: sbatch/prokka.sh
        braker3:
          file: sbatch/braker3.sh
        best-result:
          file: sbatch/bestResult.sh
        interpro:
          file: sbatch/interpro.sh
        postprocessing:
          file: sbatch/postprocessing.sh
        repeatmodeler:
          file: sbatch/repeatmodeler.sh
        transposonpsi:
          file: sbatch/transposonpsi.sh
        bedtools:
          file: sbatch/bedtools.sh
        edta:
          file: sbatch/edta.sh
        vsearch:
          file: sbatch/vsearch.sh
    wraps: c3sfr1-ssh