yeyuan98/rna_fish_analysis
RNA-FISH analysis snakemake workflow
Overview
Topics:
Latest release: None, Last update: 2022-09-12
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/yeyuan98/rna_fish_analysis . --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
To run the workflow using apptainer
/singularity
, use
snakemake --cores all --sdm apptainer
To run the workflow using a combination of conda
and apptainer
/singularity
for software deployment, use
snakemake --cores all --sdm conda apptainer
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
.
General settings
Input data organization
Configuration file
Linting and formatting
Linting results
1Lints for snakefile /tmp/tmph59bhiu5/workflow/Snakefile:
2 * Path composition with '+' in line 3:
3 This becomes quickly unreadable. Usually, it is better to endure some
4 redundancy against having a more readable workflow. Hence, just repeat
5 common prefixes. If path composition is unavoidable, use pathlib or
6 (python >= 3.6) string formatting with f"...".
7 Also see:
8
9
10Lints for snakefile /tmp/tmph59bhiu5/workflow/rules/fishdot.smk:
11 * Mixed rules and functions in same snakefile.:
12 Small one-liner functions used only once should be defined as lambda
13 expressions. Other functions should be collected in a common module, e.g.
14 'rules/common.smk'. This makes the workflow steps more readable.
15 Also see:
16 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
17
18Lints for snakefile /tmp/tmph59bhiu5/workflow/rules/segmentation.smk:
19 * Mixed rules and functions in same snakefile.:
20 Small one-liner functions used only once should be defined as lambda
21 expressions. Other functions should be collected in a common module, e.g.
22 'rules/common.smk'. This makes the workflow steps more readable.
23 Also see:
24 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
25
26Lints for snakefile /tmp/tmph59bhiu5/workflow/rules/integration_summarize.smk:
27 * Mixed rules and functions in same snakefile.:
28 Small one-liner functions used only once should be defined as lambda
29 expressions. Other functions should be collected in a common module, e.g.
30 'rules/common.smk'. This makes the workflow steps more readable.
31 Also see:
32 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
33
34Lints for rule sample_convert (line 24, /tmp/tmph59bhiu5/workflow/rules/sample_convert.smk):
35 * No log directive defined:
36 Without a log directive, all output will be printed to the terminal. In
37 distributed environments, this means that errors are harder to discover.
38 In local environments, output of concurrent jobs will be mixed and become
39 unreadable.
40 Also see:
41 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
42
43Lints for rule sample_singlechannel (line 17, /tmp/tmph59bhiu5/workflow/rules/sample_singlechannel.smk):
44 * No log directive defined:
45 Without a log directive, all output will be printed to the terminal. In
46 distributed environments, this means that errors are harder to discover.
47 In local environments, output of concurrent jobs will be mixed and become
48 unreadable.
49 Also see:
50 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
51
52Lints for rule fishdot (line 20, /tmp/tmph59bhiu5/workflow/rules/fishdot.smk):
53 * No log directive defined:
54 Without a log directive, all output will be printed to the terminal. In
55 distributed environments, this means that errors are harder to discover.
56 In local environments, output of concurrent jobs will be mixed and become
57 unreadable.
58 Also see:
59 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
60
61Lints for rule segmentation (line 20, /tmp/tmph59bhiu5/workflow/rules/segmentation.smk):
62 * No log directive defined:
63 Without a log directive, all output will be printed to the terminal. In
64 distributed environments, this means that errors are harder to discover.
65 In local environments, output of concurrent jobs will be mixed and become
66 unreadable.
67 Also see:
68 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
69
70Lints for rule integration_summarize (line 21, /tmp/tmph59bhiu5/workflow/rules/integration_summarize.smk):
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
79Lints for rule integration_overlap (line 59, /tmp/tmph59bhiu5/workflow/rules/integration_summarize.smk):
80 * No log directive defined:
81 Without a log directive, all output will be printed to the terminal. In
82 distributed environments, this means that errors are harder to discover.
83 In local environments, output of concurrent jobs will be mixed and become
84 unreadable.
85 Also see:
86 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
87
88Lints for rule integration_countPlot (line 3, /tmp/tmph59bhiu5/workflow/rules/integration_processing.smk):
89 * No log directive defined:
90 Without a log directive, all output will be printed to the terminal. In
91 distributed environments, this means that errors are harder to discover.
92 In local environments, output of concurrent jobs will be mixed and become
93 unreadable.
94 Also see:
95 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
96
97Lints for rule integration_qcPlot (line 45, /tmp/tmph59bhiu5/workflow/rules/integration_processing.smk):
98 * No log directive defined:
99 Without a log directive, all output will be printed to the terminal. In
100 distributed environments, this means that errors are harder to discover.
101 In local environments, output of concurrent jobs will be mixed and become
102 unreadable.
103 Also see:
104 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/integration_processing.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/sample_convert.smk": Formatted content is different from original
5[DEBUG]
6[DEBUG] In file "/tmp/tmph59bhiu5/workflow/Snakefile": Formatted content is different from original
7[DEBUG]
8[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/integration_summarize.smk": Formatted content is different from original
9[DEBUG]
10[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/sample_singlechannel.smk": Formatted content is different from original
11[DEBUG]
12[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/fishdot.smk": Formatted content is different from original
13[DEBUG]
14[DEBUG] In file "/tmp/tmph59bhiu5/workflow/rules/segmentation.smk": Formatted content is different from original
15[INFO] 7 file(s) would be changed 😬
16
17snakefmt version: 0.6.1