baerlachlan/smk-rnaseq-counts

Snakemake workflow for estimating read counts from RNA-seq data

Overview

Latest release: v1.3.2, Last update: 2025-11-10

Linting: linting: failed, Formatting: formatting: failed

Wrappers: bio/bedtools/genomecov bio/fastp bio/fastqc bio/gffread bio/reference/ensembl-annotation bio/reference/ensembl-sequence bio/rseqc/read_distribution bio/salmon/decoys bio/salmon/index bio/salmon/quant bio/samtools/faidx bio/samtools/index bio/star/align bio/star/index bio/subread/featurecounts bio/ucsc/genePredToBed bio/ucsc/gtfToGenePred

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda. 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/baerlachlan/smk-rnaseq-counts . --tag v1.3.2

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/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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_merge (line 13, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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    * Specify a conda environment or container for each rule.:
 20      This way, the used software for each specific step is documented, and the
 21      workflow can be executed on any machine without prerequisites.
 22      Also see:
 23      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 24      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 25
 26Lints for rule genome_faidx (line 25, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
 27    * No log directive defined:
 28      Without a log directive, all output will be printed to the terminal. In
 29      distributed environments, this means that errors are harder to discover.
 30      In local environments, output of concurrent jobs will be mixed and become
 31      unreadable.
 32      Also see:
 33      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 34
 35Lints for rule genome_chrom_sizes (line 36, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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    * Specify a conda environment or container for each rule.:
 44      This way, the used software for each specific step is documented, and the
 45      workflow can be executed on any machine without prerequisites.
 46      Also see:
 47      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 48      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 49
 50Lints for rule transcriptome_get (line 47, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
 51    * No log directive defined:
 52      Without a log directive, all output will be printed to the terminal. In
 53      distributed environments, this means that errors are harder to discover.
 54      In local environments, output of concurrent jobs will be mixed and become
 55      unreadable.
 56      Also see:
 57      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 58
 59Lints for rule transcriptome_fasta (line 59, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
 60    * No log directive defined:
 61      Without a log directive, all output will be printed to the terminal. In
 62      distributed environments, this means that errors are harder to discover.
 63      In local environments, output of concurrent jobs will be mixed and become
 64      unreadable.
 65      Also see:
 66      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 67
 68Lints for rule transcriptome_merge (line 72, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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    * Specify a conda environment or container for each rule.:
 77      This way, the used software for each specific step is documented, and the
 78      workflow can be executed on any machine without prerequisites.
 79      Also see:
 80      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 81      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 82
 83Lints for rule annotation_get (line 84, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
 84    * No log directive defined:
 85      Without a log directive, all output will be printed to the terminal. In
 86      distributed environments, this means that errors are harder to discover.
 87      In local environments, output of concurrent jobs will be mixed and become
 88      unreadable.
 89      Also see:
 90      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 91
 92Lints for rule annotation_merge (line 96, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
 93    * No log directive defined:
 94      Without a log directive, all output will be printed to the terminal. In
 95      distributed environments, this means that errors are harder to discover.
 96      In local environments, output of concurrent jobs will be mixed and become
 97      unreadable.
 98      Also see:
 99      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
100    * Specify a conda environment or container for each rule.:
101      This way, the used software for each specific step is documented, and the
102      workflow can be executed on any machine without prerequisites.
103      Also see:
104      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
105      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
106
107Lints for rule annotation_sort (line 108, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.smk):
108    * No log directive defined:
109      Without a log directive, all output will be printed to the terminal. In
110      distributed environments, this means that errors are harder to discover.
111      In local environments, output of concurrent jobs will be mixed and become
112      unreadable.
113      Also see:
114      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
115    * Specify a conda environment or container for each rule.:
116      This way, the used software for each specific step is documented, and the
117      workflow can be executed on any machine without prerequisites.
118      Also see:
119      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
120      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
121
122Lints for rule annotation_genePred (line 119, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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 annotation_bed (line 130, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/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 annotation_intergenic (line 141, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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 annotation_exon (line 157, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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 annotation_intron (line 172, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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 star_index (line 190, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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 salmon_decoy (line 203, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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 salmon_index (line 214, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/refs.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
194Lints for rule fastqc_raw (line 1, /tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/fastqc.smk):
195    * No log directive defined:
196      Without a log directive, all output will be printed to the terminal. In
197      distributed environments, this means that errors are harder to discover.
198      In local environments, output of concurrent jobs will be mixed and become
199      unreadable.
200      Also see:
201
202... (truncated)

Formatting results

 1[DEBUG] 
 2[DEBUG] In file "/tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/align.smk":  Formatted content is different from original
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12[DEBUG] In file "/tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/deduplicate.smk":  Formatted content is different from original
13[DEBUG] 
14[DEBUG] In file "/tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/common.smk":  Formatted content is different from original
15[DEBUG] 
16[DEBUG] 
17[DEBUG] 
18[DEBUG] In file "/tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/rseqc.smk":  Formatted content is different from original
19[DEBUG] 
20[DEBUG] In file "/tmp/tmp1x3u279p/baerlachlan-smk-rnaseq-counts-708ef4e/workflow/rules/rrna.smk":  Formatted content is different from original
21[DEBUG] 
22[INFO] 8 file(s) would be changed 😬
23[INFO] 5 file(s) would be left unchanged 🎉
24
25snakefmt version: 0.11.2