simonmoulds/uk-decadal-flood-prediction-lstm
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Overview
Topics:
Latest release: None, Last update: 2022-09-01
Linting: linting: failed, Formatting: formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.
When using Mamba, run
mamba create -c conda-forge -c bioconda --name snakemake snakemake snakedeploy
to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via
conda activate snakemake
Step 2: Deploy workflow
With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:
mkdir -p path/to/project-workdir
cd path/to/project-workdir
In all following steps, we will assume that you are inside of that directory. Then run
snakedeploy deploy-workflow https://github.com/simonmoulds/uk-decadal-flood-prediction-lstm . --tag None
Snakedeploy will create two folders, workflow
and config
. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.
Step 3: Configure workflow
To configure the workflow, adapt config/config.yml
to your needs following the instructions below.
Step 4: Run workflow
The deployment method is controlled using the --software-deployment-method
(short --sdm
) argument.
To run the workflow with automatic deployment of all required software via conda
/mamba
, use
snakemake --cores all --sdm conda
Snakemake will automatically detect the main Snakefile
in the workflow
subfolder and execute the workflow module that has been defined by the deployment in step 2.
For further options such as cluster and cloud execution, see the docs.
Step 5: Generate report
After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using
snakemake --report report.zip
Configuration
The following section is imported from the workflow’s config/README.md
.
Describe how to configure the workflow (using config.yaml and maybe additional files). All of them need to be present with example entries inside of the config folder.
Linting and formatting
Linting results
1Lints for rule obs_input (line 31, /tmp/tmp8k5x7agg/workflow/Snakefile):
2 * No log directive defined:
3 Without a log directive, all output will be printed to the terminal. In
4 distributed environments, this means that errors are harder to discover.
5 In local environments, output of concurrent jobs will be mixed and become
6 unreadable.
7 Also see:
8 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
9 * Param outputdir is a prefix of input or output file but hardcoded:
10 If this is meant to represent a file path prefix, it will fail when
11 running workflow in environments without a shared filesystem. Instead,
12 provide a function that infers the appropriate prefix from the input or
13 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
14 Also see:
15 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
16 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
17
18Lints for rule mod_input (line 63, /tmp/tmp8k5x7agg/workflow/Snakefile):
19 * No log directive defined:
20 Without a log directive, all output will be printed to the terminal. In
21 distributed environments, this means that errors are harder to discover.
22 In local environments, output of concurrent jobs will be mixed and become
23 unreadable.
24 Also see:
25 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
26
27Lints for rule select_stations (line 93, /tmp/tmp8k5x7agg/workflow/Snakefile):
28 * No log directive defined:
29 Without a log directive, all output will be printed to the terminal. In
30 distributed environments, this means that errors are harder to discover.
31 In local environments, output of concurrent jobs will be mixed and become
32 unreadable.
33 Also see:
34 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
35
36Lints for rule get_discharge_data (line 121, /tmp/tmp8k5x7agg/workflow/Snakefile):
37 * No log directive defined:
38 Without a log directive, all output will be printed to the terminal. In
39 distributed environments, this means that errors are harder to discover.
40 In local environments, output of concurrent jobs will be mixed and become
41 unreadable.
42 Also see:
43 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
44 * Param outputdir is a prefix of input or output file but hardcoded:
45 If this is meant to represent a file path prefix, it will fail when
46 running workflow in environments without a shared filesystem. Instead,
47 provide a function that infers the appropriate prefix from the input or
48 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
49 Also see:
50 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
51 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
52
53Lints for rule nao_matching (line 154, /tmp/tmp8k5x7agg/workflow/Snakefile):
54 * No log directive defined:
55 Without a log directive, all output will be printed to the terminal. In
56 distributed environments, this means that errors are harder to discover.
57 In local environments, output of concurrent jobs will be mixed and become
58 unreadable.
59 Also see:
60 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
61 * Param outputdir is a prefix of input or output file but hardcoded:
62 If this is meant to represent a file path prefix, it will fail when
63 running workflow in environments without a shared filesystem. Instead,
64 provide a function that infers the appropriate prefix from the input or
65 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
66 Also see:
67 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
68 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
69
70Lints for rule build_catchment_dataset (line 193, /tmp/tmp8k5x7agg/workflow/Snakefile):
71 * No log directive defined:
72 Without a log directive, all output will be printed to the terminal. In
73 distributed environments, this means that errors are harder to discover.
74 In local environments, output of concurrent jobs will be mixed and become
75 unreadable.
76 Also see:
77 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
78 * Param outputdir is a prefix of input or output file but hardcoded:
79 If this is meant to represent a file path prefix, it will fail when
80 running workflow in environments without a shared filesystem. Instead,
81 provide a function that infers the appropriate prefix from the input or
82 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
83 Also see:
84 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
85 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
86
87Lints for rule fit_gamlss_models (line 230, /tmp/tmp8k5x7agg/workflow/Snakefile):
88 * No log directive defined:
89 Without a log directive, all output will be printed to the terminal. In
90 distributed environments, this means that errors are harder to discover.
91 In local environments, output of concurrent jobs will be mixed and become
92 unreadable.
93 Also see:
94 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
95 * Param outputdir is a prefix of input or output file but hardcoded:
96 If this is meant to represent a file path prefix, it will fail when
97 running workflow in environments without a shared filesystem. Instead,
98 provide a function that infers the appropriate prefix from the input or
99 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
100 Also see:
101 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
102 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
103
104Lints for rule prepare_nh_input (line 263, /tmp/tmp8k5x7agg/workflow/Snakefile):
105 * No log directive defined:
106 Without a log directive, all output will be printed to the terminal. In
107 distributed environments, this means that errors are harder to discover.
108 In local environments, output of concurrent jobs will be mixed and become
109 unreadable.
110 Also see:
111 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
112 * Param outputdir is a prefix of input or output file but hardcoded:
113 If this is meant to represent a file path prefix, it will fail when
114 running workflow in environments without a shared filesystem. Instead,
115 provide a function that infers the appropriate prefix from the input or
116 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
117 Also see:
118 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
119 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
120
121Lints for rule run_nh (line 299, /tmp/tmp8k5x7agg/workflow/Snakefile):
122 * No log directive defined:
123 Without a log directive, all output will be printed to the terminal. In
124 distributed environments, this means that errors are harder to discover.
125 In local environments, output of concurrent jobs will be mixed and become
126 unreadable.
127 Also see:
128 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmp8k5x7agg/workflow/Snakefile": Formatted content is different from original
3[INFO] 1 file(s) would be changed 😬
4
5snakefmt version: 0.6.1