baerlachlan/smk-rnaseq-gatk-variants
Snakemake implementation of the GATK best-practices workflow for RNA-seq short variant discovery
Overview
Topics:
Latest release: v1.0.3, Last update: 2024-08-22
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-gatk-variants . --tag v1.0.3
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
.
The workflow requires configuration by modification of config/config.yaml
.
Follow the explanations provided as comments in the file.
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).
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.
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
1Lints for rule genome_get (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
2 * No log directive defined:
3 Without a log directive, all output will be printed to the terminal. In
4 distributed environments, this means that errors are harder to discover.
5 In local environments, output of concurrent jobs will be mixed and become
6 unreadable.
7 Also see:
8 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
9
10Lints for rule genome_index (line 26, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
11 * No log directive defined:
12 Without a log directive, all output will be printed to the terminal. In
13 distributed environments, this means that errors are harder to discover.
14 In local environments, output of concurrent jobs will be mixed and become
15 unreadable.
16 Also see:
17 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
18
19Lints for rule genome_dict (line 53, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
20 * No log directive defined:
21 Without a log directive, all output will be printed to the terminal. In
22 distributed environments, this means that errors are harder to discover.
23 In local environments, output of concurrent jobs will be mixed and become
24 unreadable.
25 Also see:
26 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
27
28Lints for rule annotation_get (line 80, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
29 * No log directive defined:
30 Without a log directive, all output will be printed to the terminal. In
31 distributed environments, this means that errors are harder to discover.
32 In local environments, output of concurrent jobs will be mixed and become
33 unreadable.
34 Also see:
35 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
36
37Lints for rule star_index (line 105, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
38 * No log directive defined:
39 Without a log directive, all output will be printed to the terminal. In
40 distributed environments, this means that errors are harder to discover.
41 In local environments, output of concurrent jobs will be mixed and become
42 unreadable.
43 Also see:
44 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
45
46Lints for rule known_variants_get (line 134, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
47 * No log directive defined:
48 Without a log directive, all output will be printed to the terminal. In
49 distributed environments, this means that errors are harder to discover.
50 In local environments, output of concurrent jobs will be mixed and become
51 unreadable.
52 Also see:
53 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
54
55Lints for rule known_variants_index (line 164, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/refs.smk):
56 * No log directive defined:
57 Without a log directive, all output will be printed to the terminal. In
58 distributed environments, this means that errors are harder to discover.
59 In local environments, output of concurrent jobs will be mixed and become
60 unreadable.
61 Also see:
62 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
63
64Lints for rule gtf_to_bed (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):
65 * No log directive defined:
66 Without a log directive, all output will be printed to the terminal. In
67 distributed environments, this means that errors are harder to discover.
68 In local environments, output of concurrent jobs will be mixed and become
69 unreadable.
70 Also see:
71 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
72
73Lints for rule bed_to_intervals (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/intervals.smk):
74 * No log directive defined:
75 Without a log directive, all output will be printed to the terminal. In
76 distributed environments, this means that errors are harder to discover.
77 In local environments, output of concurrent jobs will be mixed and become
78 unreadable.
79 Also see:
80 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
81
82Lints for rule fastqc_raw (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):
83 * No log directive defined:
84 Without a log directive, all output will be printed to the terminal. In
85 distributed environments, this means that errors are harder to discover.
86 In local environments, output of concurrent jobs will be mixed and become
87 unreadable.
88 Also see:
89 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
90
91Lints for rule fastqc_trim (line 29, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):
92 * No log directive defined:
93 Without a log directive, all output will be printed to the terminal. In
94 distributed environments, this means that errors are harder to discover.
95 In local environments, output of concurrent jobs will be mixed and become
96 unreadable.
97 Also see:
98 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
99
100Lints for rule fastqc_align (line 57, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/fastqc.smk):
101 * No log directive defined:
102 Without a log directive, all output will be printed to the terminal. In
103 distributed environments, this means that errors are harder to discover.
104 In local environments, output of concurrent jobs will be mixed and become
105 unreadable.
106 Also see:
107 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
108
109Lints for rule trim_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):
110 * No log directive defined:
111 Without a log directive, all output will be printed to the terminal. In
112 distributed environments, this means that errors are harder to discover.
113 In local environments, output of concurrent jobs will be mixed and become
114 unreadable.
115 Also see:
116 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
117
118Lints for rule trim_pe (line 30, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):
119 * No log directive defined:
120 Without a log directive, all output will be printed to the terminal. In
121 distributed environments, this means that errors are harder to discover.
122 In local environments, output of concurrent jobs will be mixed and become
123 unreadable.
124 Also see:
125 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
126
127Lints for rule trim_md5 (line 64, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/trim.smk):
128 * No log directive defined:
129 Without a log directive, all output will be printed to the terminal. In
130 distributed environments, this means that errors are harder to discover.
131 In local environments, output of concurrent jobs will be mixed and become
132 unreadable.
133 Also see:
134 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
135 * Specify a conda environment or container for each rule.:
136 This way, the used software for each specific step is documented, and the
137 workflow can be executed on any machine without prerequisites.
138 Also see:
139 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
140 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
141
142Lints for rule align (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):
143 * No log directive defined:
144 Without a log directive, all output will be printed to the terminal. In
145 distributed environments, this means that errors are harder to discover.
146 In local environments, output of concurrent jobs will be mixed and become
147 unreadable.
148 Also see:
149 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
150
151Lints for rule align_md5 (line 31, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk):
152 * No log directive defined:
153 Without a log directive, all output will be printed to the terminal. In
154 distributed environments, this means that errors are harder to discover.
155 In local environments, output of concurrent jobs will be mixed and become
156 unreadable.
157 Also see:
158 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
159 * Specify a conda environment or container for each rule.:
160 This way, the used software for each specific step is documented, and the
161 workflow can be executed on any machine without prerequisites.
162 Also see:
163 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
164 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
165
166Lints for rule assign_read_groups (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):
167 * No log directive defined:
168 Without a log directive, all output will be printed to the terminal. In
169 distributed environments, this means that errors are harder to discover.
170 In local environments, output of concurrent jobs will be mixed and become
171 unreadable.
172 Also see:
173 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
174
175Lints for rule assign_read_groups_index (line 28, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):
176 * No log directive defined:
177 Without a log directive, all output will be printed to the terminal. In
178 distributed environments, this means that errors are harder to discover.
179 In local environments, output of concurrent jobs will be mixed and become
180 unreadable.
181 Also see:
182 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
183
184Lints for rule assign_read_groups_md5 (line 50, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/assign_read_groups.smk):
185 * No log directive defined:
186 Without a log directive, all output will be printed to the terminal. In
187 distributed environments, this means that errors are harder to discover.
188 In local environments, output of concurrent jobs will be mixed and become
189 unreadable.
190 Also see:
191 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
192 * Specify a conda environment or container for each rule.:
193 This way, the used software for each specific step is documented, and the
194 workflow can be executed on any machine without prerequisites.
195 Also see:
196 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
197 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
198
199Lints for rule group_umis_se (line 1, /tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/group_umis.smk):
200 * No log directive defined:
201
202... (truncated)
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12[DEBUG] In file "/tmp/tmpq65g3tiz/baerlachlan-smk-rnaseq-gatk-variants-9ad4331/workflow/rules/align.smk": Formatted content is different from original
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17
18snakefmt version: 0.10.2