loganylchen/NanoRNAMod

None

Overview

Latest release: v0.1.5, Last update: 2026-05-19

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=loganylchen/NanoRNAMod

Quality control: linting: failed formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --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

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

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 v0.1.5

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.

Workflow parameters

The following table is automatically parsed from the workflow’s config.schema.y(a)ml file.

Parameter

Type

Description

Required

Default

samples

string

yes

project

string

yes

reference

yes

. transcriptome_fasta

string

yes

. genome_fasta

string

. transcriptome_gtf

string

tools

yes

. xpore

. . activate

boolean

. nanocompore

. . activate

boolean

params

yes

. minimap2

string

. samtools_filtering

string

. f5c_eventalign_full

string

. f5c_eventalign_simple

string

. nanocompore

string

threads

yes

. minimap2

integer

. multi_to_single

integer

. tombo_lsc

integer

. tombo_msc

integer

. tombo_resquiggle

integer

. slow5tools

integer

. f5c

integer

. m6anet

integer

. nanocompore

integer

Linting and formatting

Linting results
  1/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile:196: SyntaxWarning: invalid escape sequence '\d'
  2  sample="[\da-zA-Z]+_?[0-9]*",
  3/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile:197: SyntaxWarning: invalid escape sequence '\d'
  4  control="[\da-zA-Z]+_?[0-9]*",
  5/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile:198: SyntaxWarning: invalid escape sequence '\d'
  6  native="[\da-zA-Z]+_?[0-9]*",
  7/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile:201: SyntaxWarning: invalid escape sequence '\d'
  8  project="[\da-zA-Z]+_?[0-9]*",
  9No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#'
 10Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
 11Note that schema file may not be validated correctly.
 12No validator found for JSON Schema version identifier 'http://json-schema.org/draft-06/schema#'
 13Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
 14Note that schema file may not be validated correctly.
 15============================================================
 16NanoRNAMod — Active tools summary
 17  Comparison tools (1): pybaleen
 18  Per-sample tools (0): none
 19  Inactive tools   (6): xpore, nanocompore, differr, drummer, eligos2, epinano
 20  Samples: A, B, F
 21  Comparisons: A_F, B_F
 22============================================================
 23Lints for snakefile /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile:
 24    * Absolute path "/scratch/..." in line 227:
 25      Do not define absolute paths inside of the workflow, since this renders
 26      your workflow irreproducible on other machines. Use path relative to the
 27      working directory instead, or make the path configurable via a config
 28      file.
 29      Also see:
 30      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 31    * Environment variable TMPDIR used but not asserted with envvars directive in line 217.:
 32      Asserting existence of environment variables with the envvars directive
 33      ensures proper error messages if the user fails to invoke a workflow with
 34      all required environment variables defined. Further, it allows snakemake
 35      to pass them on in case of distributed execution.
 36      Also see:
 37      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables
 38    * Environment variable TMPDIR used but not asserted with envvars directive in line 224.:
 39      Asserting existence of environment variables with the envvars directive
 40      ensures proper error messages if the user fails to invoke a workflow with
 41      all required environment variables defined. Further, it allows snakemake
 42      to pass them on in case of distributed execution.
 43      Also see:
 44      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#environment-variables
 45    * Mixed rules and functions in same snakefile.:
 46      Small one-liner functions used only once should be defined as lambda
 47      expressions. Other functions should be collected in a common module, e.g.
 48      'rules/common.smk'. This makes the workflow steps more readable.
 49      Also see:
 50      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 51
 52Lints for snakefile /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/common.smk:
 53    * Mixed rules and functions in same snakefile.:
 54      Small one-liner functions used only once should be defined as lambda
 55      expressions. Other functions should be collected in a common module, e.g.
 56      'rules/common.smk'. This makes the workflow steps more readable.
 57      Also see:
 58      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 59
 60Lints for rule workflow_version (line 183, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/common.smk):
 61    * No log directive defined:
 62      Without a log directive, all output will be printed to the terminal. In
 63      distributed environments, this means that errors are harder to discover.
 64      In local environments, output of concurrent jobs will be mixed and become
 65      unreadable.
 66      Also see:
 67      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 68    * Migrate long run directives into scripts or notebooks:
 69      Long run directives hamper workflow readability. Use the script or
 70      notebook directive instead. Note that the script or notebook directive
 71      does not involve boilerplate. Similar to run, you will have direct access
 72      to params, input, output, and wildcards.Only use the run directive for a
 73      handful of lines.
 74      Also see:
 75      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts
 76      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration
 77
 78Lints for rule link_fastq (line 6, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_data_prep.smk):
 79    * Specify a conda environment or container for each rule.:
 80      This way, the used software for each specific step is documented, and the
 81      workflow can be executed on any machine without prerequisites.
 82      Also see:
 83      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 84      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 85
 86Lints for rule link_blow5 (line 32, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_data_prep.smk):
 87    * Specify a conda environment or container for each rule.:
 88      This way, the used software for each specific step is documented, and the
 89      workflow can be executed on any machine without prerequisites.
 90      Also see:
 91      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 92      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 93
 94Lints for rule xpore_run (line 58, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_xpore.smk):
 95    * Do not access input and output files individually by index in shell commands:
 96      When individual access to input or output files is needed (i.e., just
 97      writing '{input}' is impossible), use names ('{input.somename}') instead
 98      of index based access.
 99      Also see:
100      https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules
101
102Lints for rule prep_drummer_region (line 1, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_drummer.smk):
103    * No log directive defined:
104      Without a log directive, all output will be printed to the terminal. In
105      distributed environments, this means that errors are harder to discover.
106      In local environments, output of concurrent jobs will be mixed and become
107      unreadable.
108      Also see:
109      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
110
111Lints for rule eligos2_prep (line 41, /tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_eligos2.smk):
112    * No log directive defined:
113      Without a log directive, all output will be printed to the terminal. In
114      distributed environments, this means that errors are harder to discover.
115      In local environments, output of concurrent jobs will be mixed and become
116      unreadable.
117      Also see:
118      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_nanocompore.smk":  Formatted content is different from original
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 5[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_pybaleen.smk":  Formatted content is different from original
 6[DEBUG] 
 7[WARNING] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_drummer.smk":  Keyword "output" at line 39 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[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_drummer.smk":  Formatted content is different from original
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17[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_index_f5c.smk":  Formatted content is different from original
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20[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_reference.smk":  Formatted content is different from original
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23[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_xpore.smk":  Formatted content is different from original
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25[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/polya_estimate_nanopolish.smk":  Formatted content is different from original
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27[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/modetect_epinano.smk":  Formatted content is different from original
28[DEBUG] 
29[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_data_prep.smk":  Formatted content is different from original
30[DEBUG] 
31[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_align_minimap2.smk":  Formatted content is different from original
32[DEBUG] 
33<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
34<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
35<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
36<unknown>:1: SyntaxWarning: invalid escape sequence '\d'
37[WARNING] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile":  Keyword "input" at line 275 has comments under a value.
38	PEP8 recommends block comments appear before what they describe
39(see https://www.python.org/dev/peps/pep-0008/#id30)
40[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/Snakefile":  Formatted content is different from original
41[DEBUG] 
42[DEBUG] 
43[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/prep_eventalign_f5c.smk":  Formatted content is different from original
44[DEBUG] 
45[DEBUG] In file "/tmp/tmpc1urpb32/loganylchen-NanoRNAMod-30e62bd/workflow/rules/common.smk":  Formatted content is different from original
46[DEBUG] 
47[INFO] 15 file(s) would be changed 😬
48[INFO] 6 file(s) would be left unchanged 🎉
49
50snakefmt version: 0.11.5