koesterlab/rossi-ips-dmr
Calling and plotting of differentially methylated regions between two or more biological samples in BAM format
Overview
Topics:
Latest release: None, Last update: 2025-06-26
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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/koesterlab/rossi-ips-dmr . --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.
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1Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).
2Workflow defines that rule get_gene_elements_annotation is eligible for caching between workflows (use the --cache argument to enable this).
3Lints for snakefile /tmp/tmpexe8bu7h/workflow/Snakefile:
4 * Absolute path "/homes/aprinz/enrichment/workflow/Snakefile" in line 46:
5 Do not define absolute paths inside of the workflow, since this renders
6 your workflow irreproducible on other machines. Use path relative to the
7 working directory instead, or make the path configurable via a config
8 file.
9 Also see:
10 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
11
12Lints for snakefile https://:raw.githubusercontent.com/Addimator/enrichment/main/workflow/rules/datavzrd.smk:
13 * Mixed rules and functions in same snakefile.:
14 Small one-liner functions used only once should be defined as lambda
15 expressions. Other functions should be collected in a common module, e.g.
16 'rules/common.smk'. This makes the workflow steps more readable.
17 Also see:
18 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
19
20Lints for rule download_metilene (line 3, /tmp/tmpexe8bu7h/workflow/rules/dmr_calling.smk):
21 * No log directive defined:
22 Without a log directive, all output will be printed to the terminal. In
23 distributed environments, this means that errors are harder to discover.
24 In local environments, output of concurrent jobs will be mixed and become
25 unreadable.
26 Also see:
27 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
28
29Lints for rule unpack_metilene (line 12, /tmp/tmpexe8bu7h/workflow/rules/dmr_calling.smk):
30 * No log directive defined:
31 Without a log directive, all output will be printed to the terminal. In
32 distributed environments, this means that errors are harder to discover.
33 In local environments, output of concurrent jobs will be mixed and become
34 unreadable.
35 Also see:
36 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
37
38Lints for rule call_metilene (line 40, /tmp/tmpexe8bu7h/workflow/rules/dmr_calling.smk):
39 * No log directive defined:
40 Without a log directive, all output will be printed to the terminal. In
41 distributed environments, this means that errors are harder to discover.
42 In local environments, output of concurrent jobs will be mixed and become
43 unreadable.
44 Also see:
45 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
46
47Lints for rule plot_dmrs (line 75, /tmp/tmpexe8bu7h/workflow/rules/dmr_calling.smk):
48 * No log directive defined:
49 Without a log directive, all output will be printed to the terminal. In
50 distributed environments, this means that errors are harder to discover.
51 In local environments, output of concurrent jobs will be mixed and become
52 unreadable.
53 Also see:
54 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
55
56Lints for rule most_variable_positions (line 36, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
57 * No log directive defined:
58 Without a log directive, all output will be printed to the terminal. In
59 distributed environments, this means that errors are harder to discover.
60 In local environments, output of concurrent jobs will be mixed and become
61 unreadable.
62 Also see:
63 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
64
65Lints for rule scatter_plot (line 47, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
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
74Lints for rule scatter_plot_pb_np (line 74, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
75 * No log directive defined:
76 Without a log directive, all output will be printed to the terminal. In
77 distributed environments, this means that errors are harder to discover.
78 In local environments, output of concurrent jobs will be mixed and become
79 unreadable.
80 Also see:
81 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
82
83Lints for rule scatter_plot_endo_meso (line 90, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
84 * No log directive defined:
85 Without a log directive, all output will be printed to the terminal. In
86 distributed environments, this means that errors are harder to discover.
87 In local environments, output of concurrent jobs will be mixed and become
88 unreadable.
89 Also see:
90 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
91
92Lints for rule pluripotency_score_psc (line 116, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
93 * No log directive defined:
94 Without a log directive, all output will be printed to the terminal. In
95 distributed environments, this means that errors are harder to discover.
96 In local environments, output of concurrent jobs will be mixed and become
97 unreadable.
98 Also see:
99 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
100
101Lints for rule pluripotency_score_all (line 136, /tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk):
102 * No log directive defined:
103 Without a log directive, all output will be printed to the terminal. In
104 distributed environments, this means that errors are harder to discover.
105 In local environments, output of concurrent jobs will be mixed and become
106 unreadable.
107 Also see:
108 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
109
110Lints for rule index_alignment (line 49, /tmp/tmpexe8bu7h/workflow/rules/prepare_meth_calling.smk):
111 * No log directive defined:
112 Without a log directive, all output will be printed to the terminal. In
113 distributed environments, this means that errors are harder to discover.
114 In local environments, output of concurrent jobs will be mixed and become
115 unreadable.
116 Also see:
117 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
118
119Lints for rule pb_CpG_rename_output (line 37, /tmp/tmpexe8bu7h/workflow/rules/pbCpgTools.smk):
120 * No log directive defined:
121 Without a log directive, all output will be printed to the terminal. In
122 distributed environments, this means that errors are harder to discover.
123 In local environments, output of concurrent jobs will be mixed and become
124 unreadable.
125 Also see:
126 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
127
128Lints for rule compute_meth_observations (line 50, /tmp/tmpexe8bu7h/workflow/rules/methylation_calling.smk):
129 * No log directive defined:
130 Without a log directive, all output will be printed to the terminal. In
131 distributed environments, this means that errors are harder to discover.
132 In local environments, output of concurrent jobs will be mixed and become
133 unreadable.
134 Also see:
135 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
136
137Lints for rule call_methylation (line 73, /tmp/tmpexe8bu7h/workflow/rules/methylation_calling.smk):
138 * No log directive defined:
139 Without a log directive, all output will be printed to the terminal. In
140 distributed environments, this means that errors are harder to discover.
141 In local environments, output of concurrent jobs will be mixed and become
142 unreadable.
143 Also see:
144 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
145
146Lints for rule filter_calls (line 90, /tmp/tmpexe8bu7h/workflow/rules/methylation_calling.smk):
147 * No log directive defined:
148 Without a log directive, all output will be printed to the terminal. In
149 distributed environments, this means that errors are harder to discover.
150 In local environments, output of concurrent jobs will be mixed and become
151 unreadable.
152 Also see:
153 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
154
155Lints for rule calls_to_vcf (line 108, /tmp/tmpexe8bu7h/workflow/rules/methylation_calling.smk):
156 * No log directive defined:
157 Without a log directive, all output will be printed to the terminal. In
158 distributed environments, this means that errors are harder to discover.
159 In local environments, output of concurrent jobs will be mixed and become
160 unreadable.
161 Also see:
162 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
163
164Lints for rule gather_calls (line 122, /tmp/tmpexe8bu7h/workflow/rules/methylation_calling.smk):
165 * No log directive defined:
166 Without a log directive, all output will be printed to the terminal. In
167 distributed environments, this means that errors are harder to discover.
168 In local environments, output of concurrent jobs will be mixed and become
169 unreadable.
170 Also see:
171 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
172
173Lints for rule rna_seq_annotations (line 28, /tmp/tmpexe8bu7h/workflow/rules/compare_rna.smk):
174 * No log directive defined:
175 Without a log directive, all output will be printed to the terminal. In
176 distributed environments, this means that errors are harder to discover.
177 In local environments, output of concurrent jobs will be mixed and become
178 unreadable.
179 Also see:
180 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
181
182Lints for rule download_regulatory_elements (line 1, /tmp/tmpexe8bu7h/workflow/rules/annotate_dmrs.smk):
183 * No log directive defined:
184 Without a log directive, all output will be printed to the terminal. In
185 distributed environments, this means that errors are harder to discover.
186 In local environments, output of concurrent jobs will be mixed and become
187 unreadable.
188 Also see:
189 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
190
191Lints for rule annotate_regulatory_elements (line 16, /tmp/tmpexe8bu7h/workflow/rules/annotate_dmrs.smk):
192 * No log directive defined:
193 Without a log directive, all output will be printed to the terminal. In
194 distributed environments, this means that errors are harder to discover.
195 In local environments, output of concurrent jobs will be mixed and become
196 unreadable.
197 Also see:
198 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
199
200Lints for rule add_regulatory_elements_header (line 30, /tmp/tmpexe8bu7h/workflow/rules/annotate_dmrs.smk):
201
202... (truncated)
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4[WARNING] In file "/tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk": Keyword "input" at line 6 has comments under a value.
5 PEP8 recommends block comments appear before what they describe
6(see https://www.python.org/dev/peps/pep-0008/#id30)
7[WARNING] In file "/tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk": Keyword "input" at line 48 has comments under a value.
8 PEP8 recommends block comments appear before what they describe
9(see https://www.python.org/dev/peps/pep-0008/#id30)
10[ERROR] In file "/tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk": NoParametersError: L84: In wildcard_constraints definition.
11[DEBUG] In file "/tmp/tmpexe8bu7h/workflow/rules/plots_paper.smk":
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18[WARNING] In file "/tmp/tmpexe8bu7h/workflow/Snakefile": Keyword "snakefile" at line 39 has comments under a value.
19 PEP8 recommends block comments appear before what they describe
20(see https://www.python.org/dev/peps/pep-0008/#id30)
21[DEBUG] In file "/tmp/tmpexe8bu7h/workflow/Snakefile": Formatted content is different from original
22[DEBUG]
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24[WARNING] In file "/tmp/tmpexe8bu7h/workflow/rules/pbCpgTools.smk": Keyword "input" at line 38 has comments under a value.
25 PEP8 recommends block comments appear before what they describe
26(see https://www.python.org/dev/peps/pep-0008/#id30)
27[DEBUG] In file "/tmp/tmpexe8bu7h/workflow/rules/pbCpgTools.smk": Formatted content is different from original
28[DEBUG]
29[INFO] 1 file(s) raised parsing errors 🤕
30[INFO] 3 file(s) would be changed 😬
31[INFO] 8 file(s) would be left unchanged 🎉
32
33snakefmt version: 0.11.0