jjjoelle/learn_rna

None

Overview

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