loganylchen/NanoRNAMod
None
Overview
Topics:
Latest release: None, Last update: 2024-05-24
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/loganylchen/NanoRNAMod . --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
1/tmp/tmphbho_a5c/workflow/Snakefile:10: SyntaxWarning: invalid escape sequence '\d'
2 sample="[\da-zA-Z]+_?[\d]*",
3/tmp/tmphbho_a5c/workflow/Snakefile:11: SyntaxWarning: invalid escape sequence '\d'
4 control="[\da-zA-Z]+_?[\d]*",
5/tmp/tmphbho_a5c/workflow/Snakefile:12: SyntaxWarning: invalid escape sequence '\d'
6 native="[\da-zA-Z]+_?[\d]*",
7/tmp/tmphbho_a5c/workflow/Snakefile:13: SyntaxWarning: invalid escape sequence '\d'
8 sample_size="[\d]+",
9/tmp/tmphbho_a5c/workflow/Snakefile:14: SyntaxWarning: invalid escape sequence '\d'
10 n="[\d]+"
11Traceback (most recent call last):
12
13 File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py", line 1983, in args_to_api
14 any_lint = workflow_api.lint()
15 ^^^^^^^^^^^^^^^^^^^
16
17 File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py", line 337, in _handle_no_dag
18 return method(self, *args, **kwargs)
19 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
20
21 File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py", line 354, in lint
22 workflow.include(
23
24 File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py", line 1398, in include
25 exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
26
27 File "/tmp/tmphbho_a5c/workflow/Snakefile", line 76, in <module>
28
29 File "/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py", line 1398, in include
30 exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
31
32 File "/tmp/tmphbho_a5c/workflow/rules/modetect_eligos2.smk", line 24, in <module>
33 "-t {threads} "
34 ^^^^^
35
36KeyError: 'eligos2'
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_differr.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_nanocompore.smk": Formatted content is different from original
5[DEBUG]
6[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_reference.smk": Formatted content is different from original
7[DEBUG]
8<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
9<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
10<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
11<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
12<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
13[WARNING] In file "/tmp/tmphbho_a5c/workflow/Snakefile": Keyword "input" at line 57 has comments under a value.
14 PEP8 recommends block comments appear before what they describe
15(see https://www.python.org/dev/peps/pep-0008/#id30)
16[DEBUG] In file "/tmp/tmphbho_a5c/workflow/Snakefile": Formatted content is different from original
17[DEBUG]
18[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_readsfiltering.smk": Formatted content is different from original
19[DEBUG]
20[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_align_minimap2.smk": Formatted content is different from original
21[DEBUG]
22[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/common.smk": Formatted content is different from original
23[DEBUG]
24[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_eligos2.smk": Formatted content is different from original
25[DEBUG]
26[WARNING] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_drummer.smk": Keyword "output" at line 46 has comments under a value.
27 PEP8 recommends block comments appear before what they describe
28(see https://www.python.org/dev/peps/pep-0008/#id30)
29[WARNING] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_drummer.smk": Keyword "output" at line 69 has comments under a value.
30 PEP8 recommends block comments appear before what they describe
31(see https://www.python.org/dev/peps/pep-0008/#id30)
32[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_drummer.smk": Formatted content is different from original
33[DEBUG]
34[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_baleen.smk": Formatted content is different from original
35[DEBUG]
36[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_data_prep.smk": Formatted content is different from original
37[DEBUG]
38[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_eventalign_f5c.smk": Formatted content is different from original
39[DEBUG]
40[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/prep_index_f5c.smk": Formatted content is different from original
41[DEBUG]
42[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/qc_quantification_nanocount.smk": Formatted content is different from original
43[DEBUG]
44[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_xpore.smk": Formatted content is different from original
45[DEBUG]
46[WARNING] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_epinano.smk": Keyword "output" at line 9 has comments under a value.
47 PEP8 recommends block comments appear before what they describe
48(see https://www.python.org/dev/peps/pep-0008/#id30)
49[WARNING] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_epinano.smk": Keyword "output" at line 35 has comments under a value.
50 PEP8 recommends block comments appear before what they describe
51(see https://www.python.org/dev/peps/pep-0008/#id30)
52[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/modetect_epinano.smk": Formatted content is different from original
53[DEBUG]
54[DEBUG] In file "/tmp/tmphbho_a5c/workflow/rules/post_format.smk": Formatted content is different from original
55[INFO] 17 file(s) would be changed 😬
56
57snakefmt version: 0.10.2