tmweiskittel/tmwalign

None

Overview

Latest release: None, Last update: 2026-03-29

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=tmweiskittel/tmwalign

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/tmweiskittel/tmwalign . --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 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

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.

Workflow overview

This workflow is a best-practice workflow for <detailed description>. The workflow is built using snakemake and consists of the following steps:

  1. Download genome reference from NCBI

  2. Validate downloaded genome (python script)

  3. Simulate short read sequencing data on the fly (dwgsim)

  4. Check quality of input read data (FastQC)

  5. Collect statistics from tool output (MultiQC)

Running the workflow

Input data

This template workflow creates artificial sequencing data in *.fastq.gz format. It does not contain actual input data. The simulated input files are nevertheless created based on a mandatory table linked in the config.yaml file (default: .test/samples.tsv). The sample sheet has the following layout:

sample

condition

replicate

read1

read2

sample1

wild_type

1

sample1.bwa.read1.fastq.gz

sample1.bwa.read2.fastq.gz

sample2

wild_type

2

sample2.bwa.read1.fastq.gz

sample2.bwa.read2.fastq.gz

Parameters

This table lists all parameters that can be used to run the workflow.

parameter

type

details

default

sample_sheet

path

str

path to sample sheet, mandatory

“config/samples.tsv”

get_genome

ncbi_ftp

str

link to a genome on NCBI’s FTP server

link to S. cerevisiae genome

simulate_reads

read_length

num

length of target reads in bp

100

read_number

num

number of total reads to be simulated

10000

Workflow parameters

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

Parameter

Type

Description

Required

Default

sample_sheet

string

path to sample-sheet TSV file

yes

get_genome

yes

. ncbi_ftp

string

URL for genome retrieval

yes

simulate_reads

yes

. read_length

number

length of target reads in bp

. read_number

number

number of total reads to be simulated

Linting and formatting

Linting results
  1Lints for snakefile /tmp/tmp2p9863tf/workflow/Snakefile:
  2    * Mixed rules and functions in same snakefile.:
  3      Small one-liner functions used only once should be defined as lambda
  4      expressions. Other functions should be collected in a common module, e.g.
  5      'rules/common.smk'. This makes the workflow steps more readable.
  6      Also see:
  7      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
  8
  9Lints for rule unpack_hg38 (line 6, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 10    * Specify a conda environment or container for each rule.:
 11      This way, the used software for each specific step is documented, and the
 12      workflow can be executed on any machine without prerequisites.
 13      Also see:
 14      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 15      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 16
 17Lints for rule organize_blacklist (line 19, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 18    * Specify a conda environment or container for each rule.:
 19      This way, the used software for each specific step is documented, and the
 20      workflow can be executed on any machine without prerequisites.
 21      Also see:
 22      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 23      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 24
 25Lints for rule normalize_spikein_headers (line 32, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 26    * Specify a conda environment or container for each rule.:
 27      This way, the used software for each specific step is documented, and the
 28      workflow can be executed on any machine without prerequisites.
 29      Also see:
 30      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 31      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 32
 33Lints for rule download_reference_files (line 52, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 34    * Specify a conda environment or container for each rule.:
 35      This way, the used software for each specific step is documented, and the
 36      workflow can be executed on any machine without prerequisites.
 37      Also see:
 38      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 39      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 40    * Shell command directly uses variable REF_SOURCE from outside of the rule:
 41      It is recommended to pass all files as input and output, and non-file
 42      parameters via the params directive. Otherwise, provenance tracking is
 43      less accurate.
 44      Also see:
 45      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 46    * Shell command directly uses variable REF_FASTA from outside of the rule:
 47      It is recommended to pass all files as input and output, and non-file
 48      parameters via the params directive. Otherwise, provenance tracking is
 49      less accurate.
 50      Also see:
 51      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 52    * Shell command directly uses variable REF_BED from outside of the rule:
 53      It is recommended to pass all files as input and output, and non-file
 54      parameters via the params directive. Otherwise, provenance tracking is
 55      less accurate.
 56      Also see:
 57      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 58    * Shell command directly uses variable REF_BWA from outside of the rule:
 59      It is recommended to pass all files as input and output, and non-file
 60      parameters via the params directive. Otherwise, provenance tracking is
 61      less accurate.
 62      Also see:
 63      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 64
 65Lints for rule download_metadata (line 76, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 66    * Specify a conda environment or container for each rule.:
 67      This way, the used software for each specific step is documented, and the
 68      workflow can be executed on any machine without prerequisites.
 69      Also see:
 70      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 71      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 72    * Shell command directly uses variable LOCAL_PATH from outside of the rule:
 73      It is recommended to pass all files as input and output, and non-file
 74      parameters via the params directive. Otherwise, provenance tracking is
 75      less accurate.
 76      Also see:
 77      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 78    * Shell command directly uses variable LOCAL_PATH from outside of the rule:
 79      It is recommended to pass all files as input and output, and non-file
 80      parameters via the params directive. Otherwise, provenance tracking is
 81      less accurate.
 82      Also see:
 83      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 84
 85Lints for rule bwa_index_reference (line 93, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 86    * Shell command directly uses variable REF_BWA from outside of the rule:
 87      It is recommended to pass all files as input and output, and non-file
 88      parameters via the params directive. Otherwise, provenance tracking is
 89      less accurate.
 90      Also see:
 91      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 92
 93Lints for rule build_combined_reference (line 116, /tmp/tmp2p9863tf/workflow/rules/references_combined.smk):
 94    * Specify a conda environment or container for each rule.:
 95      This way, the used software for each specific step is documented, and the
 96      workflow can be executed on any machine without prerequisites.
 97      Also see:
 98      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 99      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
100
101Lints for rule download_fastqs (line 1, /tmp/tmp2p9863tf/workflow/rules/download_samples.smk):
102    * Specify a conda environment or container for each rule.:
103      This way, the used software for each specific step is documented, and the
104      workflow can be executed on any machine without prerequisites.
105      Also see:
106      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
107      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
108    * Shell command directly uses variable FASTQ_DIR from outside of the rule:
109      It is recommended to pass all files as input and output, and non-file
110      parameters via the params directive. Otherwise, provenance tracking is
111      less accurate.
112      Also see:
113      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
114    * Shell command directly uses variable LOCAL_PATH from outside of the rule:
115      It is recommended to pass all files as input and output, and non-file
116      parameters via the params directive. Otherwise, provenance tracking is
117      less accurate.
118      Also see:
119      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
120
121Lints for rule fastp_trim (line 1, /tmp/tmp2p9863tf/workflow/rules/fastp_trimming.smk):
122    * Shell command directly uses variable TRIMMED_DIR from outside of the rule:
123      It is recommended to pass all files as input and output, and non-file
124      parameters via the params directive. Otherwise, provenance tracking is
125      less accurate.
126      Also see:
127      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
128    * Shell command directly uses variable QC_DIR from outside of the rule:
129      It is recommended to pass all files as input and output, and non-file
130      parameters via the params directive. Otherwise, provenance tracking is
131      less accurate.
132      Also see:
133      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
134    * Shell command directly uses variable LOCAL_PATH from outside of the rule:
135      It is recommended to pass all files as input and output, and non-file
136      parameters via the params directive. Otherwise, provenance tracking is
137      less accurate.
138      Also see:
139      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
140
141Lints for rule bwameth_align (line 1, /tmp/tmp2p9863tf/workflow/rules/alignment.smk):
142    * Shell command directly uses variable BAM_DIR from outside of the rule:
143      It is recommended to pass all files as input and output, and non-file
144      parameters via the params directive. Otherwise, provenance tracking is
145      less accurate.
146      Also see:
147      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
148    * Shell command directly uses variable LOCAL_PATH from outside of the rule:
149      It is recommended to pass all files as input and output, and non-file
150      parameters via the params directive. Otherwise, provenance tracking is
151      less accurate.
152      Also see:
153      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
Formatting results
 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmp2p9863tf/workflow/Snakefile":  Formatted content is different from original
 3[DEBUG] 
 4[DEBUG] In file "/tmp/tmp2p9863tf/workflow/rules/download_samples.smk":  Formatted content is different from original
 5[DEBUG] 
 6[DEBUG] In file "/tmp/tmp2p9863tf/workflow/rules/references_combined.smk":  Formatted content is different from original
 7[DEBUG] 
 8[DEBUG] In file "/tmp/tmp2p9863tf/workflow/rules/fastp_trimming.smk":  Formatted content is different from original
 9[DEBUG] 
10[DEBUG] In file "/tmp/tmp2p9863tf/workflow/rules/alignment.smk":  Formatted content is different from original
11[INFO] 5 file(s) would be changed 😬
12
13snakefmt version: 0.11.5