baerlachlan/smk-rnaseq-counts

Snakemake workflow for estimating read counts from RNA-seq data

Overview

Latest release: v1.3.1, Last update: 2025-07-16

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/baerlachlan/smk-rnaseq-counts . --tag v1.3.1

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.

Configuration

Workflow config

The workflow requires configuration by modification of config/config.yaml. Follow the explanations provided as comments in the file.

Sample & unit config

The configuration of samples and units is specified as tab-separated value (.tsv) files. Each .tsv requires specific columns (see below), but extra columns may be present (however, will not be used).

samples.tsv

The default path for the sample sheet is config/samples.tsv. This may be changed via configuration in config/config.yaml.

samples.tsv requires only one column named sample, which contains the desired names of the samples. Sample names must be unique, corresponding to a physical sample. Biological and technical replicates should be specified as separate samples.

units.tsv

The default path for the unit sheet is config/units.tsv. This may be changed via configuration in config/config.yaml.

units.tsv requires four columns, named sample, unit, fq1 and fq2. Each row of the units sheet corresponds to a single sequencing unit. Therefore, for each sample specified in samples.tsv, one or more sequencing units should be present. unit values must be unique within each sample. A common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.

For each unit, the respective path to FASTQ files must be specified in the fq1 and fq2 columns. Both columns must exist, however, the fq2 column may be left empty in the case of single-end sequencing experiments. This is how one specifies whether single- or paired-end rules are run by the workflow.

Linting and formatting

Linting results

  1Using workflow specific profile workflow/profiles/default for setting default command line arguments.
  2Lints for rule genome_get (line 1, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
  3    * No log directive defined:
  4      Without a log directive, all output will be printed to the terminal. In
  5      distributed environments, this means that errors are harder to discover.
  6      In local environments, output of concurrent jobs will be mixed and become
  7      unreadable.
  8      Also see:
  9      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 10
 11Lints for rule genome_faidx (line 13, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 12    * No log directive defined:
 13      Without a log directive, all output will be printed to the terminal. In
 14      distributed environments, this means that errors are harder to discover.
 15      In local environments, output of concurrent jobs will be mixed and become
 16      unreadable.
 17      Also see:
 18      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 19
 20Lints for rule genome_chrom_sizes (line 24, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 21    * No log directive defined:
 22      Without a log directive, all output will be printed to the terminal. In
 23      distributed environments, this means that errors are harder to discover.
 24      In local environments, output of concurrent jobs will be mixed and become
 25      unreadable.
 26      Also see:
 27      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 28    * Specify a conda environment or container for each rule.:
 29      This way, the used software for each specific step is documented, and the
 30      workflow can be executed on any machine without prerequisites.
 31      Also see:
 32      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 33      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 34
 35Lints for rule transcriptome_get (line 35, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 36    * No log directive defined:
 37      Without a log directive, all output will be printed to the terminal. In
 38      distributed environments, this means that errors are harder to discover.
 39      In local environments, output of concurrent jobs will be mixed and become
 40      unreadable.
 41      Also see:
 42      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 43
 44Lints for rule annotation_get (line 47, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 45    * No log directive defined:
 46      Without a log directive, all output will be printed to the terminal. In
 47      distributed environments, this means that errors are harder to discover.
 48      In local environments, output of concurrent jobs will be mixed and become
 49      unreadable.
 50      Also see:
 51      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 52
 53Lints for rule annotation_sort (line 59, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 54    * No log directive defined:
 55      Without a log directive, all output will be printed to the terminal. In
 56      distributed environments, this means that errors are harder to discover.
 57      In local environments, output of concurrent jobs will be mixed and become
 58      unreadable.
 59      Also see:
 60      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 61    * Specify a conda environment or container for each rule.:
 62      This way, the used software for each specific step is documented, and the
 63      workflow can be executed on any machine without prerequisites.
 64      Also see:
 65      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 66      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 67
 68Lints for rule annotation_genePred (line 70, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 69    * No log directive defined:
 70      Without a log directive, all output will be printed to the terminal. In
 71      distributed environments, this means that errors are harder to discover.
 72      In local environments, output of concurrent jobs will be mixed and become
 73      unreadable.
 74      Also see:
 75      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 76
 77Lints for rule annotation_bed (line 81, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 78    * No log directive defined:
 79      Without a log directive, all output will be printed to the terminal. In
 80      distributed environments, this means that errors are harder to discover.
 81      In local environments, output of concurrent jobs will be mixed and become
 82      unreadable.
 83      Also see:
 84      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 85
 86Lints for rule annotation_intergenic (line 92, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 87    * No log directive defined:
 88      Without a log directive, all output will be printed to the terminal. In
 89      distributed environments, this means that errors are harder to discover.
 90      In local environments, output of concurrent jobs will be mixed and become
 91      unreadable.
 92      Also see:
 93      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 94
 95Lints for rule annotation_exon (line 108, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
 96    * No log directive defined:
 97      Without a log directive, all output will be printed to the terminal. In
 98      distributed environments, this means that errors are harder to discover.
 99      In local environments, output of concurrent jobs will be mixed and become
100      unreadable.
101      Also see:
102      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
103
104Lints for rule annotation_intron (line 123, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
105    * No log directive defined:
106      Without a log directive, all output will be printed to the terminal. In
107      distributed environments, this means that errors are harder to discover.
108      In local environments, output of concurrent jobs will be mixed and become
109      unreadable.
110      Also see:
111      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
112
113Lints for rule star_index (line 141, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
114    * No log directive defined:
115      Without a log directive, all output will be printed to the terminal. In
116      distributed environments, this means that errors are harder to discover.
117      In local environments, output of concurrent jobs will be mixed and become
118      unreadable.
119      Also see:
120      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
121
122Lints for rule salmon_decoy (line 154, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
123    * No log directive defined:
124      Without a log directive, all output will be printed to the terminal. In
125      distributed environments, this means that errors are harder to discover.
126      In local environments, output of concurrent jobs will be mixed and become
127      unreadable.
128      Also see:
129      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
130
131Lints for rule salmon_index (line 165, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/refs.smk):
132    * No log directive defined:
133      Without a log directive, all output will be printed to the terminal. In
134      distributed environments, this means that errors are harder to discover.
135      In local environments, output of concurrent jobs will be mixed and become
136      unreadable.
137      Also see:
138      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
139
140Lints for rule fastqc_raw (line 1, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/fastqc.smk):
141    * No log directive defined:
142      Without a log directive, all output will be printed to the terminal. In
143      distributed environments, this means that errors are harder to discover.
144      In local environments, output of concurrent jobs will be mixed and become
145      unreadable.
146      Also see:
147      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
148
149Lints for rule fastqc_trim (line 13, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/fastqc.smk):
150    * No log directive defined:
151      Without a log directive, all output will be printed to the terminal. In
152      distributed environments, this means that errors are harder to discover.
153      In local environments, output of concurrent jobs will be mixed and become
154      unreadable.
155      Also see:
156      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
157
158Lints for rule fastqc_align (line 25, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/fastqc.smk):
159    * No log directive defined:
160      Without a log directive, all output will be printed to the terminal. In
161      distributed environments, this means that errors are harder to discover.
162      In local environments, output of concurrent jobs will be mixed and become
163      unreadable.
164      Also see:
165      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
166
167Lints for rule trim_se (line 1, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/trim.smk):
168    * No log directive defined:
169      Without a log directive, all output will be printed to the terminal. In
170      distributed environments, this means that errors are harder to discover.
171      In local environments, output of concurrent jobs will be mixed and become
172      unreadable.
173      Also see:
174      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
175
176Lints for rule trim_pe (line 14, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/trim.smk):
177    * No log directive defined:
178      Without a log directive, all output will be printed to the terminal. In
179      distributed environments, this means that errors are harder to discover.
180      In local environments, output of concurrent jobs will be mixed and become
181      unreadable.
182      Also see:
183      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
184
185Lints for rule merge (line 1, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/merge.smk):
186    * No log directive defined:
187      Without a log directive, all output will be printed to the terminal. In
188      distributed environments, this means that errors are harder to discover.
189      In local environments, output of concurrent jobs will be mixed and become
190      unreadable.
191      Also see:
192      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
193    * Specify a conda environment or container for each rule.:
194      This way, the used software for each specific step is documented, and the
195      workflow can be executed on any machine without prerequisites.
196      Also see:
197      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
198      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
199
200Lints for rule align (line 1, /tmp/tmpc4phljzu/baerlachlan-smk-rnaseq-counts-d138506/workflow/rules/align.smk):
201
202... (truncated)

Formatting results

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22[INFO] 8 file(s) would be changed 😬
23[INFO] 5 file(s) would be left unchanged 🎉
24
25snakefmt version: 0.11.0