jjjoelle/learn_rna
None
Overview
Topics:
Latest release: None, Last update: 2023-01-10
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/jjjoelle/learn_rna . --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
.
configure Snakemake enviroment
'mamba env -f snake.yaml'
Currently there is no adjustable config.yaml file
Linting and formatting
Linting results
1Lints for snakefile /tmp/tmpbpa_m3_j/workflow/Snakefile:
2 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/reads/a.chr21.1.fq" in line 3:
3 Do not define absolute paths inside of the workflow, since this renders
4 your workflow irreproducible on other machines. Use path relative to the
5 working directory instead, or make the path configurable via a config
6 file.
7 Also see:
8 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
9 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/reads/a.chr21.2.fq" in line 3:
10 Do not define absolute paths inside of the workflow, since this renders
11 your workflow irreproducible on other machines. Use path relative to the
12 working directory instead, or make the path configurable via a config
13 file.
14 Also see:
15 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
16 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/reads/b.chr21.1.fq" in line 3:
17 Do not define absolute paths inside of the workflow, since this renders
18 your workflow irreproducible on other machines. Use path relative to the
19 working directory instead, or make the path configurable via a config
20 file.
21 Also see:
22 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
23 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/reads/b.chr21.2.fq" in line 3:
24 Do not define absolute paths inside of the workflow, since this renders
25 your workflow irreproducible on other machines. Use path relative to the
26 working directory instead, or make the path configurable via a config
27 file.
28 Also see:
29 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
30 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/ref/genome.chr21.fa" in line 38:
31 Do not define absolute paths inside of the workflow, since this renders
32 your workflow irreproducible on other machines. Use path relative to the
33 working directory instead, or make the path configurable via a config
34 file.
35 Also see:
36 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
37 * Absolute path "/raidixshare_logg01/jfaybishenko/github_repos/ngs-test-data/ref/annotation.chr21.gtf" in line 83:
38 Do not define absolute paths inside of the workflow, since this renders
39 your workflow irreproducible on other machines. Use path relative to the
40 working directory instead, or make the path configurable via a config
41 file.
42 Also see:
43 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
44 * Mixed rules and functions in same snakefile.:
45 Small one-liner functions used only once should be defined as lambda
46 expressions. Other functions should be collected in a common module, e.g.
47 'rules/common.smk'. This makes the workflow steps more readable.
48 Also see:
49 https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
50
51Lints for rule index (line 42, /tmp/tmpbpa_m3_j/workflow/Snakefile):
52 * Do not access input and output files individually by index in shell commands:
53 When individual access to input or output files is needed (i.e., just
54 writing '{input}' is impossible), use names ('{input.somename}') instead
55 of index based access.
56 Also see:
57 https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
58
59Lints for rule fastqc (line 69, /tmp/tmpbpa_m3_j/workflow/Snakefile):
60 * Do not access input and output files individually by index in shell commands:
61 When individual access to input or output files is needed (i.e., just
62 writing '{input}' is impossible), use names ('{input.somename}') instead
63 of index based access.
64 Also see:
65 https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
66
67Lints for rule trim (line 96, /tmp/tmpbpa_m3_j/workflow/Snakefile):
68 * Do not access input and output files individually by index in shell commands:
69 When individual access to input or output files is needed (i.e., just
70 writing '{input}' is impossible), use names ('{input.somename}') instead
71 of index based access.
72 Also see:
73 https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
74
75Lints for rule align (line 133, /tmp/tmpbpa_m3_j/workflow/Snakefile):
76 * Do not access input and output files individually by index in shell commands:
77 When individual access to input or output files is needed (i.e., just
78 writing '{input}' is impossible), use names ('{input.somename}') instead
79 of index based access.
80 Also see:
81 https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
82
83Lints for rule multiqc (line 161, /tmp/tmpbpa_m3_j/workflow/Snakefile):
84 * Do not access input and output files individually by index in shell commands:
85 When individual access to input or output files is needed (i.e., just
86 writing '{input}' is impossible), use names ('{input.somename}') instead
87 of index based access.
88 Also see:
89 https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
Formatting results
1[DEBUG]
2[WARNING] In file "/tmp/tmpbpa_m3_j/workflow/Snakefile": Keyword "shell" at line 71 has comments under a value.
3 PEP8 recommends block comments appear before what they describe
4(see https://www.python.org/dev/peps/pep-0008/#id30)
5[DEBUG] In file "/tmp/tmpbpa_m3_j/workflow/Snakefile": Formatted content is different from original
6[INFO] 1 file(s) would be changed 😬
7
8snakefmt version: 0.8.0