SchlossLab/mothur-snakemake-workflow
Snakemake template for microbial amplicon sequence analysis with mothur.
Overview
Topics: 16s-rrna mothur snakemake
Latest release: None, Last update: 2023-02-09
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/SchlossLab/mothur-snakemake-workflow . --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
.
TODO: configuration instructions
- how to run the demo (config/demo.yaml)
- how to use your own dataset (config/crc/crc.yaml)
Linting and formatting
Linting results
1Lints for snakefile /tmp/tmp2l12itn8/workflow/Snakefile:
2 * Mixed rules and functions in same snakefile.:
3 Small one-liner functions used only once should be defined as lambda
4 expressions. Other functions should be collected in a common module, e.g.
5 'rules/common.smk'. This makes the workflow steps more readable.
6 Also see:
7 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
8
9Lints for rule download_silva (line 35, /tmp/tmp2l12itn8/workflow/Snakefile):
10 * No log directive defined:
11 Without a log directive, all output will be printed to the terminal. In
12 distributed environments, this means that errors are harder to discover.
13 In local environments, output of concurrent jobs will be mixed and become
14 unreadable.
15 Also see:
16 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
17 * Specify a conda environment or container for each rule.:
18 This way, the used software for each specific step is documented, and the
19 workflow can be executed on any machine without prerequisites.
20 Also see:
21 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
22 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
23 * Param outdir is a prefix of input or output file but hardcoded:
24 If this is meant to represent a file path prefix, it will fail when
25 running workflow in environments without a shared filesystem. Instead,
26 provide a function that infers the appropriate prefix from the input or
27 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
28 Also see:
29 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
30 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
31
32Lints for rule process_silva (line 78, /tmp/tmp2l12itn8/workflow/Snakefile):
33 * Param workdir is a prefix of input or output file but hardcoded:
34 If this is meant to represent a file path prefix, it will fail when
35 running workflow in environments without a shared filesystem. Instead,
36 provide a function that infers the appropriate prefix from the input or
37 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
38 Also see:
39 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
40 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
41
42Lints for rule download_rdp (line 141, /tmp/tmp2l12itn8/workflow/Snakefile):
43 * No log directive defined:
44 Without a log directive, all output will be printed to the terminal. In
45 distributed environments, this means that errors are harder to discover.
46 In local environments, output of concurrent jobs will be mixed and become
47 unreadable.
48 Also see:
49 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
50 * Specify a conda environment or container for each rule.:
51 This way, the used software for each specific step is documented, and the
52 workflow can be executed on any machine without prerequisites.
53 Also see:
54 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
55 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
56 * Param outdir is a prefix of input or output file but hardcoded:
57 If this is meant to represent a file path prefix, it will fail when
58 running workflow in environments without a shared filesystem. Instead,
59 provide a function that infers the appropriate prefix from the input or
60 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
61 Also see:
62 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
63 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
64
65Lints for rule download_demo_data (line 182, /tmp/tmp2l12itn8/workflow/Snakefile):
66 * No log directive defined:
67 Without a log directive, all output will be printed to the terminal. In
68 distributed environments, this means that errors are harder to discover.
69 In local environments, output of concurrent jobs will be mixed and become
70 unreadable.
71 Also see:
72 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
73 * Specify a conda environment or container for each rule.:
74 This way, the used software for each specific step is documented, and the
75 workflow can be executed on any machine without prerequisites.
76 Also see:
77 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
78 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
79
80Lints for rule download_sra_data (line 212, /tmp/tmp2l12itn8/workflow/Snakefile):
81 * No log directive defined:
82 Without a log directive, all output will be printed to the terminal. In
83 distributed environments, this means that errors are harder to discover.
84 In local environments, output of concurrent jobs will be mixed and become
85 unreadable.
86 Also see:
87 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
88 * Specify a conda environment or container for each rule.:
89 This way, the used software for each specific step is documented, and the
90 workflow can be executed on any machine without prerequisites.
91 Also see:
92 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
93 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
94 * Param outdir is a prefix of input or output file but hardcoded:
95 If this is meant to represent a file path prefix, it will fail when
96 running workflow in environments without a shared filesystem. Instead,
97 provide a function that infers the appropriate prefix from the input or
98 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
99 Also see:
100 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
101 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
102
103Lints for rule process_data (line 260, /tmp/tmp2l12itn8/workflow/Snakefile):
104 * Param workdir is a prefix of input or output file but hardcoded:
105 If this is meant to represent a file path prefix, it will fail when
106 running workflow in environments without a shared filesystem. Instead,
107 provide a function that infers the appropriate prefix from the input or
108 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
109 Also see:
110 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
111 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
112
113Lints for rule calc_dists (line 365, /tmp/tmp2l12itn8/workflow/Snakefile):
114 * Param outdir is a prefix of input or output file but hardcoded:
115 If this is meant to represent a file path prefix, it will fail when
116 running workflow in environments without a shared filesystem. Instead,
117 provide a function that infers the appropriate prefix from the input or
118 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
119 Also see:
120 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
121 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
122
123Lints for rule cluster_OTUs (line 412, /tmp/tmp2l12itn8/workflow/Snakefile):
124 * Param outdir is a prefix of input or output file but hardcoded:
125 If this is meant to represent a file path prefix, it will fail when
126 running workflow in environments without a shared filesystem. Instead,
127 provide a function that infers the appropriate prefix from the input or
128 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
129 Also see:
130 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
131 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
132
133Lints for rule get_shared (line 472, /tmp/tmp2l12itn8/workflow/Snakefile):
134 * Param outdir is a prefix of input or output file but hardcoded:
135 If this is meant to represent a file path prefix, it will fail when
136 running workflow in environments without a shared filesystem. Instead,
137 provide a function that infers the appropriate prefix from the input or
138 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
139 Also see:
140 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
141 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
142
143Lints for rule calc_diversity (line 524, /tmp/tmp2l12itn8/workflow/Snakefile):
144 * Param outdir is a prefix of input or output file but hardcoded:
145 If this is meant to represent a file path prefix, it will fail when
146 running workflow in environments without a shared filesystem. Instead,
147 provide a function that infers the appropriate prefix from the input or
148 output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
149 Also see:
150 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
151 https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmp2l12itn8/workflow/Snakefile": Formatted content is different from original
3[INFO] 1 file(s) would be changed 😬
4
5snakefmt version: 0.8.1